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Selmani Z, Attard E, Lauga B, Barakat M, Ortet P, Tulumello J, Achouak W, Kaci Y, Heulin T. Culturing the desert microbiota. Front Microbiol 2023; 14:1098150. [PMID: 37113232 PMCID: PMC10126307 DOI: 10.3389/fmicb.2023.1098150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).
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Affiliation(s)
- Zakia Selmani
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Eleonore Attard
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Béatrice Lauga
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Mohamed Barakat
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Philippe Ortet
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Wafa Achouak
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Yahia Kaci
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
| | - Thierry Heulin
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
- *Correspondence: Thierry Heulin,
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Collin B, Auffan M, Doelsch E, Proux O, Kieffer I, Ortet P, Santaella C. Bacterial Metabolites and Particle Size Determine Cerium Oxide Nanomaterial Biotransformation. Environ Sci Technol 2022; 56:16838-16847. [PMID: 36350260 DOI: 10.1021/acs.est.2c05280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Soil is a major receptor of manufactured nanomaterials (NMs) following unintentional releases or intentional uses. Ceria NMs have been shown to undergo biotransformation in plant and soil organisms with a partial Ce(IV) reduction into Ce(III), but the influence of environmentally widespread soil bacteria is poorly understood. We used high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS) with an unprecedented detection limit to assess Ce speciation in a model soil bacterium (Pseudomonas brassicacearum) exposed to CeO2 NMs of different sizes and shapes. The findings revealed that the CeO2 NM's size drives the biotransformation process. No biotransformation was observed for the 31 nm CeO2 NMs, contrary to 7 and 4 nm CeO2 NMs, with a Ce reduction of 64 ± 14% and 70 ± 15%, respectively. This major reduction appeared quickly, from the early exponential bacterial growth phase. Environmentally relevant organic acid metabolites secreted by Pseudomonas, especially in the rhizosphere, were investigated. The 2-keto-gluconic and citric acid metabolites alone were able to induce a significant reduction in 4 nm CeO2 NMs. The high biotransformation measured for <7 nm NMs would affect the fate of Ce in the soil and biota.
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Affiliation(s)
- Blanche Collin
- Aix Marseille Univ, CNRS, IRD, INRAE, Coll France, CEREGE, Aix-en-Provence, France
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France
| | - Mélanie Auffan
- Aix Marseille Univ, CNRS, IRD, INRAE, Coll France, CEREGE, Aix-en-Provence, France
| | - Emmanuel Doelsch
- CIRAD, UPR Recyclage et risque, F-34398 Montpellier, France
- Recyclage et risque, Univ Montpellier, CIRAD, Montpellier, France
| | - Olivier Proux
- BM30/CRG-FAME, ESRF, Université Grenoble Alpes, CNRS, IRSTEa, Météo France, IRD, OSUG, 38000 Grenoble, France
| | - Isabelle Kieffer
- BM30/CRG-FAME, ESRF, Université Grenoble Alpes, CNRS, IRSTEa, Météo France, IRD, OSUG, 38000 Grenoble, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France
| | - Catherine Santaella
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France
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Behairi S, Baha N, Barakat M, Ortet P, Achouak W, Heulin T, Kaci Y. Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil. Extremophiles 2022; 26:18. [PMID: 35652980 DOI: 10.1007/s00792-022-01268-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/05/2022] [Indexed: 11/04/2022]
Abstract
Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total of 414 strains isolated from root tissues (RT), root-adhering soil (RAS), non-adhering rhizospheric soil (NARS) and bulk soil (BS) using different NaCl concentrations. Our data showed that halophilic and halotolerant bacterial isolates in BS and the rhizosphere belonged to 32 genera distributed in Proteobacteria (49%), Firmicutes (36%), Actinobacteria (14%) and Bacteroidetes (1%). Bacterial population size and species diversity were greatly increased in the rhizosphere (factor 100). The reservoir of diversity in BS was dominated by the genera Bacillus and Halomonas. Bacillus/Halomonas ratio decreased with the proximity to the roots from 2.2 in BS to 0.3 at the root surface. Salt screening of the strains showed that species belonging to nine genera were able to grow up to 5.1 M NaCl. Thus, we found that H. strobilaceum exerted a strong effect on the diversity of the recruited microbiota with an affinity strongly attributed to the genus Halomonas.
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Affiliation(s)
- Sabrina Behairi
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Nassima Baha
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria
| | - Mohamed Barakat
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Philippe Ortet
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Wafa Achouak
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Thierry Heulin
- Lab of Microbial Ecology of the Rhizosphere (LEMiRE), ECCOREV FR3098, UMR7265 BIAM, AMU, CEA, CNRS, 13115, Saint-Paul-lez-Durance, France
| | - Yahia Kaci
- Team of Soil Biology, Laboratory of Organisms Biology and Physiology, Faculty of Biological Sciences, University of Science and Technology Houari Boumediene (USTHB), BP 32 El Alia, 16111, Bab Ezzouar, Algiers, Algeria.
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Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, Armengaud J, Chapon V. Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. ISME J 2022; 16:705-716. [PMID: 34556817 PMCID: PMC8857325 DOI: 10.1038/s41396-021-01113-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.
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Affiliation(s)
- Nicolas Gallois
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Béatrice Alpha-Bazin
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Nicolas Bremond
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Philippe Ortet
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Laurie Piette
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Abbas Mohamad Ali
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - David Lemaire
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Pierre Legrand
- grid.426328.9Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192 Gif-sur-Yvette, France
| | - Nicolas Theodorakopoulos
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France ,grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Magali Floriani
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Laureline Février
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Christophe Den Auwer
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
| | - Pascal Arnoux
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Catherine Berthomieu
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Jean Armengaud
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Virginie Chapon
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France.
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Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, Armengaud J, Chapon V. Correction: Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. ISME J 2022; 16:902-903. [PMID: 34980889 PMCID: PMC8857231 DOI: 10.1038/s41396-021-01164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Nicolas Gallois
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Nicolas Bremond
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Philippe Ortet
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Laurie Piette
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Abbas Mohamad Ali
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - David Lemaire
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Pierre Legrand
- Synchrotron SOLEIL. L'Orme des Merisiers Saint-Aubin. BP 48, 91192, Gif-sur-Yvette, France
| | - Nicolas Theodorakopoulos
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
- IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France
| | - Magali Floriani
- IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France
| | - Laureline Février
- IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France
| | | | - Pascal Arnoux
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Catherine Berthomieu
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Virginie Chapon
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France.
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Ortet P, Fochesato S, Bitbol AF, Whitworth DE, Lalaouna D, Santaella C, Heulin T, Achouak W, Barakat M. Evolutionary history expands the range of signaling interactions in hybrid multikinase networks. Sci Rep 2021; 11:11763. [PMID: 34083699 PMCID: PMC8175716 DOI: 10.1038/s41598-021-91260-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/06/2020] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions (‘phylogenetic promiscuity’). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS–GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.
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Affiliation(s)
- Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Anne-Florence Bitbol
- CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR8237), Sorbonne Université, 75005, Paris, France.,Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - David Lalaouna
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.,CNRS, ARN UPR 9002, Université de Strasbourg, 67000, Strasbourg, France
| | - Catherine Santaella
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.
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Benidire L, El Khalloufi F, Oufdou K, Barakat M, Tulumello J, Ortet P, Heulin T, Achouak W. Phytobeneficial bacteria improve saline stress tolerance in Vicia faba and modulate microbial interaction network. Sci Total Environ 2020; 729:139020. [PMID: 32498175 DOI: 10.1016/j.scitotenv.2020.139020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 02/21/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 05/25/2023]
Abstract
Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into agricultural practices. In the present work, we examined the fate of Vicia faba microbiota structure and interaction network upon inoculation with plant-nodulating rhizobia (Rhizobium leguminosarum RhOF125) and non-nodulating strains (Paenibacillus mucilaginosus BLA7 and Ensifer meliloti RhOL1) in the presence (or absence) of saline stress. Inoculated strains significantly improved plant tolerance to saline stress, suggesting either a direct or indirect effect on the plant response to such stress. To determine the structure of microbiota associated with V. faba, samples of the root-adhering soil (RAS), and the root tissues (RT) of seedlings inoculated (or not) with equal population size of RhOF125, BLA7 and RhOL1 strains and grown in the presence (or absence) of salt, were used to profile the microbial composition by 16S rRNA gene sequencing. The inoculation did not show a significant impact on the composition of the RT microbiota or RAS microbiota. The saline stress shifted the RAS microbiota composition, which correlated with a decrease in Enterobacteriaceae and an increase in Sphingobacterium, Chryseobacterium, Stenotrophomonas, Agrobacterium and Sinorhizobium. When the microbiota of roots and RAS are considered together, the interaction networks for each treatment are quite different and display different key populations involved in community assembly. These findings indicate that upon seed inoculation, community interaction networks rather than their composition may contribute to helping plants to better tolerate environmental stresses. The way microbial populations interfere with each other can have an impact on their functions and thus on their ability to express the genes required to help plants tolerate stresses.
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Affiliation(s)
- Loubna Benidire
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco; High School of Technology Laayoune, Ibn Zohr University, Morocco
| | - Fatima El Khalloufi
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco; Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty of Khouribga, Sultan Moulay Slimane University, Beni Mellal, B.P.: 145, 25000, Khouribga, Morocco
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Mohamed Barakat
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Joris Tulumello
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Biointrant, SAS BioIntrant, 84120 Pertuis, France
| | - Philippe Ortet
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Thierry Heulin
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Wafa Achouak
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France.
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Parvez S, Khan AU, Kaur G, Barakat M, Ortet P, Mayilraj S. An insight into the genome of extensively drug-resistant and uropathogenic Citrobacter werkmanii. J Glob Antimicrob Resist 2020; 22:785-791. [PMID: 32619689 DOI: 10.1016/j.jgar.2020.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/28/2020] [Accepted: 06/18/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVE Carbapenemase-producing bacteria pose a serious public-health threat. This study was performed to understand the emergence and genetic features of NDM-producers in hospital setting. METHODS Samples were collected from a tertiary-care hospital. Isolate identification was performed by 16S rRNA sequencing. The genome of Citrobacter werkmanii (AK-8) was sequenced on an Illumina NextSeq 500 platform. Resistance determinants and pathogenicity islands were determined by ResFinder and PathogenFinder, respectively. MLST, two-component systems and transcription factors were identified by P2RP server, whilst variant calling and insertion sequence (IS) elements were determined by Galaxy and ISfinder, respectively. The genome of AK-8 was compared with uropathogenic Escherichia coli strain 536. RESULTS This is the first report on whole-genome analysis of extensively drug-resistant NDM-6-producing uropathogenic C. werkmanii ST-104. Resistance genes for all antibiotics except colistin, fosfomycin, fusidic- acid, nitroimidazole, oxazolidinones, tetracycline and glycopeptides were detected in this strain. Genome analysis of AK-8 led to the identification of the BaeSR two-component system regulating production of multidrug efflux proteins. Virulence was regulated by CpxRA, ZraRS, RstAB, UhpAB, AcrAB, RcsBc and UvrY, whereas Bar-UvrY was found to control carbon metabolism, flagellum biosynthesis and biofilm formation. The AK-8 genome encodes 21 chemoreceptors involved in colonisation and pathogenesis. Fur family transcriptional regulator, cAMP receptor protein and RpoS were found to increase the virulence of AK-8. ntBLAST analysis showed 69.60% genetic identity with E. coli 536 as an adaptive feature for survival. CONCLUSION The emergence of extensively drug-resistant pathogenic C. werkmanii is alarming and it should not be ignored as commensal.
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Affiliation(s)
- Shadab Parvez
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University (AMU), Aligarh 202 002, Uttar Pradesh, India; Central Instrumentation Facility, Jamia Millia Islamia, New Delhi 110 025, India.
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University (AMU), Aligarh 202 002, Uttar Pradesh, India.
| | - Gurwinder Kaur
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | - Mohamed Barakat
- Aix-Marseille Université, CEA, CNRS, LEMiRE, UMR 7265, BIAM, Saint-Paul-lez-Durance, France
| | - Philippe Ortet
- Aix-Marseille Université, CEA, CNRS, LEMiRE, UMR 7265, BIAM, Saint-Paul-lez-Durance, France
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
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De Luca G, Fochesato S, Lavergne J, Forest KT, Barakat M, Ortet P, Achouak W, Heulin T, Verméglio A. Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis. Sci Rep 2019; 9:16505. [PMID: 31712689 PMCID: PMC6848086 DOI: 10.1038/s41598-019-52927-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/22/2019] [Indexed: 12/27/2022] Open
Abstract
Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation, light is probably an important external signal for anticipating desiccating conditions. Six genes encoding potential light sensors were identified in strain TTB310. Two genes encode for bacteriophytochromes, while the four remaining genes encode for putative blue light receptors. We determined the spectral and photochemical properties of the two recombinant bacteriophytochromes RtBphP1 and RtBphP2. In both cases, they act as sensitive red light detectors. Cyst divisions and a complete cyst-rod-cyst cycle are the main processes in darkness, whereas rod divisions predominate in red or far-red light. Mutant phenotypes caused by the inactivation of genes encoding bacteriophytochromes or heme oxygenase clearly show that both bacteriophytochromes are involved in regulating the rod-rod division. This process could favor rapid rod divisions at sunrise, after dew formation but before the progressive onset of desiccation. Our study provides the first evidence of a light-based strategy evolved in a non-photosynthetic bacterium to exploit scarse water in a desert environment.
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Affiliation(s)
- Gilles De Luca
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Jérôme Lavergne
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France.
| | - André Verméglio
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
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10
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Achouak W, Abrouk D, Guyonnet J, Barakat M, Ortet P, Simon L, Lerondelle C, Heulin T, Haichar FEZ. Plant hosts control microbial denitrification activity. FEMS Microbiol Ecol 2019; 95:5307930. [DOI: 10.1093/femsec/fiz021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Danis Abrouk
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Julien Guyonnet
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Laurent Simon
- Université de Lyon, Université Lyon 1, UMR5023 LEHNA, CNRS, ENTPE, F‐69622 Villeurbanne Cedex, France
| | - Catherine Lerondelle
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Feth el Zahar Haichar
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
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11
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Guyonnet JP, Guillemet M, Dubost A, Simon L, Ortet P, Barakat M, Heulin T, Achouak W, Haichar FEZ. Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation. Front Plant Sci 2018; 9:1662. [PMID: 30559748 PMCID: PMC6265440 DOI: 10.3389/fpls.2018.01662] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/26/2018] [Indexed: 05/20/2023]
Abstract
Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.
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Affiliation(s)
- Julien P. Guyonnet
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Martin Guillemet
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Audrey Dubost
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Laurent Simon
- CNRS, UMR 5023 LEHNA, Univ Lyon, Université Claude Bernard Lyon 1, Université Lyon 1, ENTPE, Villeurbanne, France
| | - Philippe Ortet
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
- CNRS, FR3098 ECCOREV, Aix Marseille Univ, Aix-en-Provence, France
| | - Mohamed Barakat
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
- CNRS, FR3098 ECCOREV, Aix Marseille Univ, Aix-en-Provence, France
| | - Thierry Heulin
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
- CNRS, FR3098 ECCOREV, Aix Marseille Univ, Aix-en-Provence, France
| | - Wafa Achouak
- CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, UMR 7265 BIAM, CEA, Aix Marseille Univ, Saint-Paul-lès-Durance, France
| | - Feth el Zahar Haichar
- Laboratoire d’Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA 1418, Villeurbanne, France
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12
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Gallois N, Piette L, Ortet P, Bakarat M, Long J, Berthomieu C, Armengaud J, Chapon V, Alpha-Bazin B. Proteomics data for characterizing Microbacterium oleivorans A9, an uranium-tolerant actinobacterium isolated near the Chernobyl nuclear power plant. Data Brief 2018; 21:1125-1129. [PMID: 30456224 PMCID: PMC6231083 DOI: 10.1016/j.dib.2018.10.136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/02/2017] [Revised: 03/05/2018] [Accepted: 10/25/2018] [Indexed: 11/09/2022] Open
Abstract
Microbacterium oleivorans A9 cells were exposed or not to 10 µM uranyl nitrate as resting cells in sodium chloride solution. Bacteria exposed to U(VI) and controls were harvested after 0.5, 4, and 24 h of toxicant exposure. Bacteria were subjected to high-throughput proteomics analysis using a Q-Exactive HF high resolution tandem mass spectrometer incorporating an ultra-high-field orbitrap analyzer. MS/MS spectra were assigned with a protein sequence database derived from a draft genome obtained by Illumina sequencing and systematic six-reading frame translation of all the contigs. Proteins identified in bacteria exposed to U(VI) and controls at the three time points allow defining the proteome dynamics upon uranium stress. The data reported here are related to a published study regarding the proteome dynamics of M. oleivorans A9 upon uranium stress by Gallois et al. (in press) entitled “Proteogenomic insights into uranium tolerance of a Chernobyl׳s Microbacterium bacterial isolate”. The data accompanying the manuscript describing the database searches and comparative analysis have been deposited to the ProteomeXchange with identifier PXD005794.
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Affiliation(s)
- Nicolas Gallois
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Laurie Piette
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Philippe Ortet
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d׳écologie microbienne de la rhizosphère et d׳environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Mohamed Bakarat
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d׳écologie microbienne de la rhizosphère et d׳environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Justine Long
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d׳écologie microbienne de la rhizosphère et d׳environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Catherine Berthomieu
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- CEA, DRF/Joliot/SPI/Li2D, BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Virginie Chapon
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
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13
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Ouertani A, Chaabouni I, Mosbah A, Long J, Barakat M, Mansuelle P, Mghirbi O, Najjari A, Ouzari HI, Masmoudi AS, Maresca M, Ortet P, Gigmes D, Mabrouk K, Cherif A. Two New Secreted Proteases Generate a Casein-Derived Antimicrobial Peptide in Bacillus cereus Food Born Isolate Leading to Bacterial Competition in Milk. Front Microbiol 2018; 9:1148. [PMID: 29915567 PMCID: PMC5994558 DOI: 10.3389/fmicb.2018.01148] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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] [Received: 12/26/2017] [Accepted: 05/14/2018] [Indexed: 02/05/2023] Open
Abstract
Milk and dairy products harbor a wide variety of bacterial species that compete for both limited resources and space. Under these competitive conditions, bacteria develop specialized mechanisms to protect themselves during niche colonization and nutrient acquisition processes. The bacterial antagonism mechanisms include the production of antimicrobial agents or molecules that facilitate competitor dispersal. In the present work, a bacterial strain designated RC6 was isolated from Ricotta and identified as Bacillus cereus. It generates antimicrobial peptide (AMP) when grown in the presence of casein. The AMP was active against several species of Bacillus and Listeria monocytogenes. MALDI-TOF analysis of the RP-HPLC purified fractions and amino acid sequencing revealed a molecular mass of 751 Da comprised of a 6-residue sequence, YPVEPF. BLAST analysis showed that the AMP corresponds to the fractions 114-119 of bovine β-casein and represents the product of a specific proteolysis. Analysis of the purified proteolytic fractions from the B. cereus RC6 culture supernatant indicated that the presence of at least two different endoproteases is crucial for the generation of the AMP. Indeed, we were able to identify two new candidate endoproteases by means of genome sequencing and functional assignment using a 3D structural model and molecular docking of misannotated hypothetical proteins. In this light, the capacity of B. cereus RC6 to generate antimicrobial peptides from casein, through the production of extracellular enzymes, presents a new model of antagonistic competition leading to niche colonization. Hence, as a dairy product contaminant, this strategy may enable proteolytic B. cereus RC6 niche specialization in milk matrices.
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Affiliation(s)
- Awatef Ouertani
- Université de la Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
- Aix Marseille University, Centre National de la Recherche Scientifique, ICR UMR 7273, Marseille, France
| | - Ines Chaabouni
- Université de la Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Amor Mosbah
- Université de la Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Justine Long
- Aix-Marseille University, CEA, Centre National de la Recherche Scientifique, LEMiRE, UMR 7265, BIAM, Saint-Paul-lez-Durance, France
| | - Mohamed Barakat
- Aix-Marseille University, CEA, Centre National de la Recherche Scientifique, LEMiRE, UMR 7265, BIAM, Saint-Paul-lez-Durance, France
| | - Pascal Mansuelle
- Aix Marseille Univ, Centre National de la Recherche Scientifique, IMM, Plate-Forme Protéomique, MaP IBiSA Labelled, Marseille, France
| | - Olfa Mghirbi
- Université de la Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
- Aix Marseille University, Centre National de la Recherche Scientifique, ICR UMR 7273, Marseille, France
| | - Afef Najjari
- Université Tunis El Manar, FST, LMBA (LR03ES03), Campus Universitaire, Tunis, Tunisia
| | - Hadda-Imene Ouzari
- Université Tunis El Manar, FST, LMBA (LR03ES03), Campus Universitaire, Tunis, Tunisia
| | - Ahmed S. Masmoudi
- Université de la Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Marc Maresca
- Aix-Marseille University, Centre National de la Recherche Scientifique, Centrale Marseille, iSm2, Marseille, France
| | - Philippe Ortet
- Aix-Marseille University, CEA, Centre National de la Recherche Scientifique, LEMiRE, UMR 7265, BIAM, Saint-Paul-lez-Durance, France
| | - Didier Gigmes
- Aix Marseille University, Centre National de la Recherche Scientifique, ICR UMR 7273, Marseille, France
| | - Kamel Mabrouk
- Aix Marseille University, Centre National de la Recherche Scientifique, ICR UMR 7273, Marseille, France
| | - Ameur Cherif
- Université de la Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
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Bernardo P, Charles-Dominique T, Barakat M, Ortet P, Fernandez E, Filloux D, Hartnady P, Rebelo TA, Cousins SR, Mesleard F, Cohez D, Yavercovski N, Varsani A, Harkins GW, Peterschmitt M, Malmstrom CM, Martin DP, Roumagnac P. Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. ISME J 2018; 12:173-184. [PMID: 29053145 PMCID: PMC5739011 DOI: 10.1038/ismej.2017.155] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 07/21/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022]
Abstract
Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8-35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.
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Affiliation(s)
- Pauline Bernardo
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Plant Pathology, Ohio State University, OARDC, Wooster, OH, USA
| | - Tristan Charles-Dominique
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Center for Integrative Conservation, Community Ecology and Conservation, Menglun, Yunnan, China
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Mohamed Barakat
- CEA, CNRS, Aix-Marseille Université, UMR 7265, LEMIRE, Saint-Paul-lez-Durance, France
| | - Philippe Ortet
- CEA, CNRS, Aix-Marseille Université, UMR 7265, LEMIRE, Saint-Paul-lez-Durance, France
| | - Emmanuel Fernandez
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Denis Filloux
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Penelope Hartnady
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine. University of Cape Town, Observatory, South Africa
| | - Tony A Rebelo
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Stephen R Cousins
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - François Mesleard
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc-Arles, France
- Institut Méditerranéen de Biodiversité et Ecologie (IMBE), UMR CNRS 7263-IRD 237, Université d'Avignon et des pays du Vaucluse, Aix-Marseille Université, IUT d’Avignon, Avignon, France
| | - Damien Cohez
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc-Arles, France
| | - Nicole Yavercovski
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc-Arles, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Structural Biology Research Unit, University of Cape Town, Observatory, South Africa
| | - Gordon W Harkins
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, South Africa
| | - Michel Peterschmitt
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Carolyn M Malmstrom
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
- Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine. University of Cape Town, Observatory, South Africa
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- BIOS, UMR BGPI CIRAD Campus International de Baillarguet, TA A-54/K, Montpellier Cedex 5 F-34398, France. E-mail
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Gallois N, Alpha-Bazin B, Ortet P, Barakat M, Piette L, Long J, Berthomieu C, Armengaud J, Chapon V. Proteogenomic insights into uranium tolerance of a Chernobyl's Microbacterium bacterial isolate. J Proteomics 2017; 177:148-157. [PMID: 29223802 DOI: 10.1016/j.jprot.2017.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance. We experimentally detected and annotated 1532 proteins and highlighted a total of 591 proteins for which abundances were significantly differing between conditions. Notably, proteins involved in phosphate and iron metabolisms show high dynamics. A large ratio of proteins more abundant upon uranyl stress, are distant from functionally-annotated known proteins, highlighting the lack of fundamental knowledge regarding numerous key molecular players from soil bacteria. BIOLOGICAL SIGNIFICANCE Microbacterium oleivorans A9 is an interesting environmental model to understand biological processes engaged in tolerance to radionuclides. Using an innovative proteogenomics approach, we explored its molecular mechanisms involved in uranium tolerance. We sequenced its genome, interpreted high-throughput proteomic data against a six-reading frame ORF database deduced from the draft genome, annotated the identified proteins and compared protein abundances from cells exposed or not to uranyl stress after a cascade search. These data show that a complex cellular response to uranium occurs in Microbacterium oleivorans A9, where one third of the experimental proteome is modified. In particular, the uranyl stress perturbed the phosphate and iron metabolic pathways. Furthermore, several transporters have been identified to be specifically associated to uranyl stress, paving the way to the development of biotechnological tools for uranium decontamination.
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Affiliation(s)
- Nicolas Gallois
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Philippe Ortet
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Mohamed Barakat
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Laurie Piette
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Justine Long
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Catherine Berthomieu
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France.
| | - Virginie Chapon
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
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16
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Sindikubwabo F, Ding S, Hussain T, Ortet P, Barakat M, Baumgarten S, Cannella D, Palencia A, Bougdour A, Belmudes L, Couté Y, Tardieux I, Botté CY, Scherf A, Hakimi MA. Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites. eLife 2017; 6:29391. [PMID: 29101771 PMCID: PMC5685513 DOI: 10.7554/elife.29391] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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] [Received: 06/07/2017] [Accepted: 11/02/2017] [Indexed: 12/22/2022] Open
Abstract
An unusual genome architecture characterizes the two related human parasitic pathogens Plasmodium falciparum and Toxoplasma gondii. A major fraction of the bulk parasite genome is packaged as transcriptionally permissive euchromatin with few loci embedded in silenced heterochromatin. Primary chromatin shapers include histone modifications at the nucleosome lateral surface close to the DNA but their mode of action remains unclear. We now identify versatile modifications at Lys31 within the globular domain of histone H4 that crucially determine genome organization and expression in Apicomplexa parasites. H4K31 acetylation at the promoter correlates with, and perhaps directly regulates, gene expression in both parasites. By contrast, monomethylated H4K31 is enriched in the core body of T. gondii active genes but inversely correlates with transcription, whereas it is unexpectedly enriched at transcriptionally inactive pericentromeric heterochromatin in P. falciparum, a region devoid of the characteristic H3K9me3 histone mark and its downstream effector HP1.
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Affiliation(s)
- Fabien Sindikubwabo
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Shuai Ding
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Tahir Hussain
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Philippe Ortet
- Aix-Marseille Univ, CEA, CNRS, UMR 7265, BIAM-LEMIRE, St-Paul-lez-Durance, France
| | - Mohamed Barakat
- Aix-Marseille Univ, CEA, CNRS, UMR 7265, BIAM-LEMIRE, St-Paul-lez-Durance, France
| | - Sebastian Baumgarten
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Dominique Cannella
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Lucid Belmudes
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Isabelle Tardieux
- Institute for Advanced Biosciences (IAB), Team Membrane and Cell Dynamics of Host Parasite Interactions, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Cyrille Y Botté
- Institute for Advanced Biosciences (IAB), Team ApicoLipid, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Artur Scherf
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
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17
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Layet C, Auffan M, Santaella C, Chevassus-Rosset C, Montes M, Ortet P, Barakat M, Collin B, Legros S, Bravin MN, Angeletti B, Kieffer I, Proux O, Hazemann JL, Doelsch E. Evidence that Soil Properties and Organic Coating Drive the Phytoavailability of Cerium Oxide Nanoparticles. Environ Sci Technol 2017; 51:9756-9764. [PMID: 28777564 DOI: 10.1021/acs.est.7b02397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The ISO-standardized RHIZOtest is used here for the first time to decipher how plant species, soil properties, and physical-chemical properties of the nanoparticles and their transformation regulate the phytoavailability of nanoparticles. Two plants, tomato and fescue, were exposed to two soils with contrasted properties: a sandy soil poor in organic matter and a clay soil rich in organic matter, both contaminated with 1, 15, and 50 mg·kg-1 of dissolved Ce2(SO4)3, bare and citrate-coated CeO2 nanoparticles. All the results demonstrate that two antagonistic soil properties controlled Ce uptake. The clay fraction enhanced the retention of the CeO2 nanoparticles and hence reduced Ce uptake, whereas the organic matter content enhanced Ce uptake. Moreover, in the soil poor in organic matter, the organic citrate coating significantly enhanced the phytoavailability of the cerium by forming smaller aggregates thereby facilitating the transport of nanoparticles to the roots. By getting rid of the dissimilarities between the root systems of the different plants and the normalizing the surfaces exposed to nanoparticles, the RHIZOtest demonstrated that the species of plant did not drive the phytoavailability, and provided evidence for soil-plant transfers at concentrations lower than those usually cited in the literature and closer to predicted environmental concentrations.
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Affiliation(s)
- Clément Layet
- Aix Marseille Univ, CNRS , IRD, Coll France, CEREGE, Aix en Provence, France
- iCEINT, International Center for the Environmental Implications of NanoTechologies, CNRS-Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
| | - Mélanie Auffan
- Aix Marseille Univ, CNRS , IRD, Coll France, CEREGE, Aix en Provence, France
- iCEINT, International Center for the Environmental Implications of NanoTechologies, CNRS-Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
| | - Catherine Santaella
- iCEINT, International Center for the Environmental Implications of NanoTechologies, CNRS-Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
- Aix Marseille Univ , CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement Extrêmes, ECCOREV FR3098, F-13108 Saint-Paul-lès-Durance, France
| | | | - Mélanie Montes
- CIRAD , UPR Recyclage et Risque, F-34398 Montpellier, France
| | - Philippe Ortet
- Aix Marseille Univ , CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement Extrêmes, ECCOREV FR3098, F-13108 Saint-Paul-lès-Durance, France
| | - Mohamed Barakat
- Aix Marseille Univ , CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement Extrêmes, ECCOREV FR3098, F-13108 Saint-Paul-lès-Durance, France
| | - Blanche Collin
- Aix Marseille Univ, CNRS , IRD, Coll France, CEREGE, Aix en Provence, France
- iCEINT, International Center for the Environmental Implications of NanoTechologies, CNRS-Duke University , Europôle de l'Arbois, 13545 Aix-en-Provence, France
| | - Samuel Legros
- CIRAD , UPR Recyclage et Risque, 18524 Dakar, Senegal
| | - Matthieu N Bravin
- CIRAD , UPR Recyclage et Risque, F-97408, Saint-Denis, Réunion, France
| | - Bernard Angeletti
- Aix Marseille Univ, CNRS , IRD, Coll France, CEREGE, Aix en Provence, France
| | - Isabelle Kieffer
- OSUG, UMS 832 CNRS-Université Grenoble Alpes , F-38041 Grenoble, France
| | - Olivier Proux
- OSUG, UMS 832 CNRS-Université Grenoble Alpes , F-38041 Grenoble, France
| | - Jean-Louis Hazemann
- Institut Néel, UPR 2940 CNRS-Université Grenoble Alpes , F-38000 Grenoble, France
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18
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Ndour PMS, Gueye M, Barakat M, Ortet P, Bertrand-Huleux M, Pablo AL, Dezette D, Chapuis-Lardy L, Assigbetsé K, Kane NA, Vigouroux Y, Achouak W, Ndoye I, Heulin T, Cournac L. Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation. Front Plant Sci 2017; 8:1288. [PMID: 28798755 PMCID: PMC5529415 DOI: 10.3389/fpls.2017.01288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/07/2017] [Indexed: 05/25/2023]
Abstract
Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structural formation is an important driver of soil fertility. Plant genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly 2-fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics increased with the "RAS/RT ratio." Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.
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Affiliation(s)
- Papa M. S. Ndour
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
- Département de Biologie Végétale, Université Cheikh Anta DiopDakar, Sénégal
| | - Mariama Gueye
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
| | - Mohamed Barakat
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Philippe Ortet
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Marie Bertrand-Huleux
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Anne-Laure Pablo
- Eco&Sols, Cirad, INRA, IRD, Montpellier SupAgro, Université de MontpellierMontpellier, France
| | - Damien Dezette
- Eco&Sols, Cirad, INRA, IRD, Montpellier SupAgro, Université de MontpellierMontpellier, France
| | - Lydie Chapuis-Lardy
- Eco&Sols, Cirad, INRA, IRD, Montpellier SupAgro, Université de MontpellierMontpellier, France
| | - Komi Assigbetsé
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
| | - Ndjido Ardo Kane
- Laboratoire National de Recherches sur les Productions Végétales, Institut Sénégalais de Recherches Agricoles, Centre de Recherche de Bel AirDakar, Senegal
| | | | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Ibrahima Ndoye
- Département de Biologie Végétale, Université Cheikh Anta DiopDakar, Sénégal
| | - Thierry Heulin
- Aix Marseille Université, CEA, CNRS, UMR7265, LEMIRE, Laboratoire d'Ecologie Microbienne de la Rhizosphère et Environnement extrêmes, ECCOREV FR3098F-13108 St Paul Les Durance, France
| | - Laurent Cournac
- IRD, UMR Eco&Sols, LMI IESOL, Centre de recherche ISRA-IRDDakar, Sénégal
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19
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Theodorakopoulos N, Février L, Barakat M, Ortet P, Christen R, Piette L, Levchuk S, Beaugelin-Seiller K, Sergeant C, Berthomieu C, Chapon V. Soil prokaryotic communities in Chernobyl waste disposal trench T22 are modulated by organic matter and radionuclide contamination. FEMS Microbiol Ecol 2017. [DOI: 10.1093/femsec/fix079] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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20
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Hamidat M, Barakat M, Ortet P, Chanéac C, Rose J, Bottero JY, Heulin T, Achouak W, Santaella C. Design Defines the Effects of Nanoceria at a Low Dose on Soil Microbiota and the Potentiation of Impacts by the Canola Plant. Environ Sci Technol 2016; 50:6892-6901. [PMID: 27243334 DOI: 10.1021/acs.est.6b01056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Soils act as nanoceria sinks via agricultural spreading and surface waters. Canola plants were grown for one month in soil spiked with nanoceria (1 mg·kg(-1)). To define the role of nanomaterials design on environmental impacts, we studied nanoceria with different sizes (3.5 or 31 nm) and coating (citrate). We measured microbial activities involved in C, N, and P cycling in the rhizosphere and unplanted soil. Bacterial community structure was analyzed in unplanted soil, rhizosphere, and plant roots by 454-pyrosequencing of the 16S rRNA gene. This revealed an impact gradient dependent on nanomaterials design, ranging from decreased microbial enzymatic activities in planted soil to alterations in bacterial community structure in roots. Particle size/aggregation was a key parameter in modulating nanoceria effects on root communities. Citrate coating lowered the impact on microbial enzymatic activities but triggered variability in the bacterial community structure near the plant root. Some nanoceria favored taxa whose closest relatives are hydrocarbon-degrading bacteria and disadvantaged taxa frequently associated in consortia with disease-suppressive activity toward plant pathogens. This work provides a basis to determine outcomes of nanoceria in soil, at a dose close to predicted environmental concentrations, and to design them to minimize these impacts.
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Affiliation(s)
- Mohamed Hamidat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Mohamed Barakat
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Philippe Ortet
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Corinne Chanéac
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- Chimie de la Matière Condensée, UMR7574, Collège de France, Université de Jussieu , Paris F-75231, France
| | - Jérome Rose
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Jean-Yves Bottero
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
- CNRS, Aix-Marseille Université, IRD, CEREGE UM34, F-13545 Aix en Provence, France
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
| | - Catherine Santaella
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and Biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA Cadarache, St-Paul-lez-Durance 13108, France
- GDRi iCEINT, International Consortium for the Environmental Implication of Nanotechnology, CNRS-Duke University , F-13545 Aix-en-Provence, France
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21
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El Khalloufi F, Oufdou K, Bertrand M, Lahrouni M, Oudra B, Ortet P, Barakat M, Heulin T, Achouak W. Microbiote shift in the Medicago sativa rhizosphere in response to cyanotoxins extract exposure. Sci Total Environ 2016; 539:135-142. [PMID: 26356186 DOI: 10.1016/j.scitotenv.2015.08.127] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 03/10/2015] [Revised: 07/06/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
The bloom-containing water bodies may have an impact due to cyanotoxins production on other microorganisms and aquatic plants. Where such water is being used for crops irrigation, the presence of cyanotoxins may also have a toxic impact on terrestrial plants and their rhizosphere microbiota. For that purpose, PCR-based 454 pyrosequencing was applied to phylogenetically characterize the bacterial community of Medicago sativa rhizosphere in response to cyanotoxins extract. This analysis revealed a wide diversity at species level, which decreased from unplanted soil to root tissues indicating that only some populations were able to compete for nutrients and niches in this selective habitat. Gemmatimonas, Actinobacteria, Deltaproteobacteria and Opitutae mainly inhabited the bulk soil, whereas, the root-adhering soil and the root tissues were inhabited by Gammaproteobacteria and Alphaproteobacteria. The proportion of these populations fluctuated in response to cyanotoxins extract exposure. Betaproteobacteria proportion increased in the three studied compartments, whereas Gammaproteobacteria proportion decreased except in the bulk soil. This study revealed the potential toxicity of cyanotoxins extract towards Actinobacteria, Gemmatimonas, Deltaproteobacteria, and Gammaproteobacteria, however Clostridia, Opitutae and bacteria related with Betaproteobacteria, were stimulated denoting their tolerance. Altogether, these data indicate that crop irrigation using cyanotoxins containing water might alter the rhizosphere functioning.
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Affiliation(s)
- Fatima El Khalloufi
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France; Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco; University Hassan 1st. Polydisciplinary Faculty of Khouribga, BP. 145, 25000 Khouribga, Morocco
| | - Khalid Oufdou
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Marie Bertrand
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Majida Lahrouni
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Brahim Oudra
- Laboratory of Biology and Biotechnology of Microorganisms, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Philippe Ortet
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Mohamed Barakat
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Thierry Heulin
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France
| | - Wafa Achouak
- CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem (LEMiRE), 13108, Saint Paul-Lez-Durance, France; CNRS, BVME UMR 7265, ECCOREV FR 3098, 13108, Saint Paul-Lez-Durance, France; Aix Marseille Université, 13284 Marseille Cedex 07, France.
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Guilbaud C, Morris CE, Barakat M, Ortet P, Berge O. Isolation and identification of Pseudomonas syringae facilitated by a PCR targeting the whole P. syringae group. FEMS Microbiol Ecol 2015; 92:fiv146. [PMID: 26610434 DOI: 10.1093/femsec/fiv146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2015] [Indexed: 11/13/2022] Open
Abstract
We present a reliable PCR-based method to avoid the biases related to identification based on the conventional phenotypes currently used in the identification of Pseudomonas syringae sensu lato, a ubiquitous environmental bacterium including plant pathogens. We identified a DNA target suitable for this purpose by applying a comparative genomic pipeline to Pseudomonas genomes. We designed primers and developed PCR conditions that led to a clean and strong PCR product from 97% of the 185 strains of P. syringae strains tested and gave a clear negative result for the 31 non-P. syringae strains tested. The sensitivity of standard PCR was determined with pure strains to be 10(6) bacteria mL(-1) or 0.4 ng of DNA μL(-1). Sensitivity could be improved with the touchdown method. The new PCR-assisted isolation of P. syringae was efficient when deployed on an environmental sample of river water as compared to the isolation based on phenotypes. This innovation eliminates the need for extensive expertise in isolating P. syringae colonies, was simpler, faster and very reliable. It will facilitate discovery of more diversity of P. syringae and research on emergence, dispersion and evolution to understand the varied functions of this environmental bacterium.
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Affiliation(s)
| | - Cindy E Morris
- INRA, UR0407 Pathologie Végétale, F-84143 Montfavet cedex, France
| | - Mohamed Barakat
- CEA, IBEB, Lab Ecol Microb Rhizosphere and Environ Extrem, Saint-Paul-lez-Durance, F-13108, France CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Philippe Ortet
- CEA, IBEB, Lab Ecol Microb Rhizosphere and Environ Extrem, Saint-Paul-lez-Durance, F-13108, France CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Odile Berge
- INRA, UR0407 Pathologie Végétale, F-84143 Montfavet cedex, France
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Abstract
The P2CS database (http://www.p2cs.org/) is a comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164 651 TCS proteins, from 2758 sequenced prokaryotic genomes. Several important new features have been added to P2CS since it was last described. Users can search P2CS via BLAST, adding hits to their cart, and homologous proteins can be aligned using MUSCLE and viewed using Jalview within P2CS. P2CS also provides phylogenetic trees based on the conserved signaling domains of the RRs and HKs from entire genomes. HK and RR trees are annotated with gene organization and domain architecture, providing insights into the evolutionary origin of the contemporary gene set. The majority of TCSs are encoded by adjacent HK and RR genes, however, ‘orphan’ unpaired TCS genes are also abundant and identifying their partner proteins is challenging. P2CS now provides paired HK and RR trees with proteins from the same genetic locus indicated. This allows the appraisal of evolutionary relationships across entire TCSs and in some cases the identification of candidate partners for orphan TCS proteins.
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Affiliation(s)
- Philippe Ortet
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - Catherine Santaella
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - Wafa Achouak
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
| | - Mohamed Barakat
- CEA, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, Saint-Paul-lez-Durance F-13108, France CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance F-13108, France Aix Marseille Université, BVME UMR7265, Marseille F-13284, France
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Barakat M, Ortet P, Whitworth DE. P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes. BMC Genomics 2013; 14:269. [PMID: 23601859 PMCID: PMC3637814 DOI: 10.1186/1471-2164-14-269] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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: 01/25/2013] [Accepted: 03/19/2013] [Indexed: 11/10/2022] Open
Abstract
Background Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotation. There is a need for user-friendly, fast and convenient tools to allow researchers to overcome the inherent variability in annotation between genome sequences. Results We have developed the web-server P2RP (Predicted Prokaryotic Regulatory Proteins), which enables users to identify and annotate TFs and TCS proteins within their sequences of interest. Users can input amino acid or genomic DNA sequences, and predicted proteins therein are scanned for the possession of DNA-binding domains and/or TCS domains. RPs identified in this manner are categorised into families, unambiguously annotated, and a detailed description of their features generated, using an integrated software pipeline. P2RP results can then be outputted in user-specified formats. Conclusion Biologists have an increasing need for fast and intuitively usable tools, which is why P2RP has been developed as an interactive system. As well as assisting experimental biologists to interrogate novel sequence data, it is hoped that P2RP will be built into genome annotation pipelines and re-annotation processes, to increase the consistency of RP annotation in public genomic sequences. P2RP is the first publicly available tool for predicting and analysing RP proteins in users’ sequences. The server is freely available and can be accessed along with documentation at http://www.p2rp.org.
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Ortet P, De Luca G, Whitworth DE, Barakat M. P2TF: a comprehensive resource for analysis of prokaryotic transcription factors. BMC Genomics 2012; 13:628. [PMID: 23153078 PMCID: PMC3532121 DOI: 10.1186/1471-2164-13-628] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [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: 09/05/2012] [Accepted: 11/11/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription factors (TFs) are DNA-binding proteins that regulate gene expression by activating or repressing transcription. Some have housekeeping roles, while others regulate the expression of specific genes in response to environmental change. The majority of TFs are multi-domain proteins, and they can be divided into families according to their domain organisation. There is a need for user-friendly, rigorous and consistent databases to allow researchers to overcome the inherent variability in annotation between genome sequences. DESCRIPTION P2TF (Predicted Prokaryotic Transcription Factors) is an integrated and comprehensive database relating to transcription factor proteins. The current version of the database contains 372,877 TFs from 1,987 completely sequenced prokaryotic genomes and 43 metagenomes. The database provides annotation, classification and visualisation of TF genes and their genetic context, providing researchers with a one-stop shop in which to investigate TFs. The P2TF database analyses TFs in both predicted proteomes and reconstituted ORFeomes, recovering approximately 3% more TF proteins than just screening predicted proteomes. Users are able to search the database with sequence or domain architecture queries, and resulting hits can be aligned to investigate evolutionary relationships and conservation of residues. To increase utility, all searches can be filtered by taxonomy, TF genes can be added to the P2TF cart, and gene lists can be exported for external analysis in a variety of formats. CONCLUSIONS P2TF is an open resource for biologists, allowing exploration of all TFs within prokaryotic genomes and metagenomes. The database enables a variety of analyses, and results are presented for user exploration as an interactive web interface, which provides different ways to access and download the data. The database is freely available at http://www.p2tf.org/.
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Affiliation(s)
- Philippe Ortet
- CEA, DSV, IBEB, SBVME, LEMiRE, Saint-Paul-lez-Durance, France
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Roumagnac P, Richaud P, Barakat M, Ortet P, Roncato MA, Heulin T, Peltier G, Achouak W, Cournac L. Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat. Microbiologyopen 2012; 1:349-61. [PMID: 23233392 PMCID: PMC3535381 DOI: 10.1002/mbo3.37] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 04/27/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 12/03/2022] Open
Abstract
Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production processes. Here, we describe a hierarchical biodiversity-based approach, including a chemochromic screening of hydrogenase activity of hundreds of bacterial strains collected from several ecosystems, followed by mass spectrometry measurements of hydrogenase activity of a selection of the H2-oxidizing bacterial strains identified during the screen. In all, 131 of 1266 strains, isolated from cereal rhizospheres and basins containing irradiating waste, were scored as H2-oxidizing bacteria, including Pseudomonas sp., Serratia sp., Stenotrophomonas sp., Enterobacter sp., Rahnella sp., Burkholderia sp., and Ralstonia sp. isolates. Four free-living N2-fixing bacteria harbored a high and oxygen-tolerant hydrogenase activity, which was not fully inhibited within entire cells up to 150–250 μmol/L O2 concentration or within soluble protein extracts up to 25–30 μmol/L. The only hydrogenase-related genes that we could reveal in these strains were of the hyc type (subunits of formate hydrogenlyase complex). The four free-living N2-fixing bacteria were closely related to Enterobacter radicincitans based on the sequences of four genes (16S rRNA, rpoB, hsp60, and hycE genes). These results should bring interesting prospects for microbial biohydrogen production and might have ecophysiological significance for bacterial adaptation to the oxic–anoxic interfaces in the rhizosphere.
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Affiliation(s)
- Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, F-34398, Montpellier Cedex-5, France
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27
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Schue M, Fekete A, Ortet P, Brutesco C, Heulin T, Schmitt-Kopplin P, Achouak W, Santaella C. Modulation of metabolism and switching to biofilm prevail over exopolysaccharide production in the response of Rhizobium alamii to cadmium. PLoS One 2011; 6:e26771. [PMID: 22096497 PMCID: PMC3212527 DOI: 10.1371/journal.pone.0026771] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [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: 07/11/2011] [Accepted: 10/03/2011] [Indexed: 11/19/2022] Open
Abstract
Heavy metals such as cadmium (Cd(2+)) affect microbial metabolic processes. Consequently, bacteria adapt by adjusting their cellular machinery. We have investigated the dose-dependent growth effects of Cd(2+) on Rhizobium alamii, an exopolysaccharide (EPS)-producing bacterium that forms a biofilm on plant roots. Adsorption isotherms show that the EPS of R. alamii binds cadmium in competition with calcium. A metabonomics approach based on ion cyclotron resonance Fourier transform mass spectrometry has showed that cadmium alters mainly the bacterial metabolism in pathways implying sugars, purine, phosphate, calcium signalling and cell respiration. We determined the influence of EPS on the bacterium response to cadmium, using a mutant of R. alamii impaired in EPS production (MSΔGT). Cadmium dose-dependent effects on the bacterial growth were not significantly different between the R. alamii wild type (wt) and MSΔGT strains. Although cadmium did not modify the quantity of EPS isolated from R. alamii, it triggered the formation of biofilm vs planktonic cells, both by R. alamii wt and by MSΔGT. Thus, it appears that cadmium toxicity could be managed by switching to a biofilm way of life, rather than producing EPS. We conclude that modulations of the bacterial metabolism and switching to biofilms prevails in the adaptation of R. alamii to cadmium. These results are original with regard to the conventional role attributed to EPS in a biofilm matrix, and the bacterial response to cadmium.
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Affiliation(s)
- Mathieu Schue
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Agnes Fekete
- Helmholtz-Zentrum Muenchen-German Research Center for Environmental Health, Institute for Ecological Chemistry, Department of BioGeochemistry and Analysis, Neuherberg, Germany
| | - Philippe Ortet
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Catherine Brutesco
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Thierry Heulin
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Philippe Schmitt-Kopplin
- Helmholtz-Zentrum Muenchen-German Research Center for Environmental Health, Institute for Ecological Chemistry, Department of BioGeochemistry and Analysis, Neuherberg, Germany
- Department for Chemical-Technical Analysis Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | - Wafa Achouak
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
| | - Catherine Santaella
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France
- CNRS, Unite Mixte Rech Biol Vegetale & Microbiol Enviro, UMR 6191, Saint-Paul-lez-Durance, France
- Université Aix Marseille, Saint-Paul-lez-Durance, France
- * E-mail:
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De Luca G, Barakat M, Ortet P, Fochesato S, Jourlin-Castelli C, Ansaldi M, Py B, Fichant G, Coutinho PM, Voulhoux R, Bastien O, Maréchal E, Henrissat B, Quentin Y, Noirot P, Filloux A, Méjean V, DuBow MS, Barras F, Barbe V, Weissenbach J, Mihalcescu I, Verméglio A, Achouak W, Heulin T. The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment. PLoS One 2011; 6:e23784. [PMID: 21912644 PMCID: PMC3164672 DOI: 10.1371/journal.pone.0023784] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [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: 06/03/2011] [Accepted: 07/25/2011] [Indexed: 11/22/2022] Open
Abstract
Ramlibacter tataouinensis TTB310(T) (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical "cyst-like" cells ("cyst-cyst" division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed.
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Affiliation(s)
- Gilles De Luca
- CEA, Lab Ecol Microbienne Rhizosphere & Environm Extre, iBEB, DSV, Saint-Paul-lez-Durance, France.
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Abstract
Alignment algorithms are powerful tools for searching for homologous proteins in databases, providing a score for each sequence present in the database. It has been well known for 20 years that the shape of the score distribution looks like an extreme value distribution. The extremely large number of times biologists face this class of distributions raises the question of the evolutionary origin of this probability law. We investigated the possibility of deriving the main properties of sequence alignment score distributions from a basic evolutionary process: a duplication-divergence protein evolution process in a sequence space. Firstly, the distribution of sequences in this space was defined with respect to the genetic distance between sequences. Secondly, we derived a basic relation between the genetic distance and the alignment score. We obtained a novel score probability distribution which is qualitatively very similar to that of Karlin-Altschul but performing better than all other previous model.
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Affiliation(s)
- Philippe Ortet
- CNRS (UMR 6191)-CEA Cadarache-Aix-Marseille Université, Laboratoire d'Ecologie Microbienne de la Rhizosphere, Institut de Biologie Environementale et Biotechnologie, CEA Cadarache, F-13108 Saint Paul-lez-Durance, France
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30
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Abstract
P2CS (http://www.p2cs.org) is a specialized database for prokaryotic two-component systems (TCSs), virtually ubiquitous signalling proteins which regulate a wide range of physiological processes. The primary aim of the database is to annotate and classify TCS proteins from completely sequenced prokaryotic genomes and metagenomes. Information within P2CS can be accessed through a variety of routes-TCS complements can be browsed by metagenome, replicon or sequence cluster (and these genesets are available for download by users). Alternatively a variety of database-wide or taxon-specific searches are supported. Each TCS protein is fully annotated with sequence-feature information including replicon context, while properties of the predicted proteins can be queried against several external prediction servers to suggest homologues, interaction networks, sub-cellular localization and domain complements. Another unique feature of P2CS is the analysis of ORFeomes to identify TCS genes missed during genome annotation. Recent innovations for P2CS include a CGView representation of the distribution of TCS genes around a replicon, categorization of TCS genes based on gene organization, an expanded domain-based classification scheme, a P2CS 'gene cart' and categorization on the basis of sequence clusters.
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Affiliation(s)
- Mohamed Barakat
- CEA, DSV, IBEB, SBVME, LEMiRE, F-13108 Saint-Paul-lez-Durance, France.
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Braun L, Cannella D, Ortet P, Barakat M, Sautel CF, Kieffer S, Garin J, Bastien O, Voinnet O, Hakimi MA. A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii. PLoS Pathog 2010; 6:e1000920. [PMID: 20523899 PMCID: PMC2877743 DOI: 10.1371/journal.ppat.1000920] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 04/23/2010] [Indexed: 12/21/2022] Open
Abstract
In RNA silencing, small RNAs produced by the RNase-III Dicer guide Argonaute-like proteins as part of RNA-induced silencing complexes (RISC) to regulate gene expression transcriptionally or post-transcriptionally. Here, we have characterized the RNA silencing machinery and exhaustive small RNAome of Toxoplasma gondii, member of the Apicomplexa, a phylum of animal- and human-infecting parasites that cause extensive health and economic damages to human populations worldwide. Remarkably, the small RNA-generating machinery of Toxoplasma is phylogenetically and functionally related to that of plants and fungi, and accounts for an exceptionally diverse array of small RNAs. This array includes conspicuous populations of repeat-associated small interfering RNA (siRNA), which, as in plants, likely generate and maintain heterochromatin at DNA repeats and satellites. Toxoplasma small RNAs also include many microRNAs with clear metazoan-like features whose accumulation is sometimes extremely high and dynamic, an unexpected finding given that Toxoplasma is a unicellular protist. Both plant-like heterochromatic small RNAs and metazoan-like microRNAs bind to a single Argonaute protein, Tg-AGO. Toxoplasma miRNAs co-sediment with polyribosomes, and thus, are likely to act as translational regulators, consistent with the lack of catalytic residues in Tg-AGO. Mass spectrometric analyses of the Tg-AGO protein complex revealed a common set of virtually all known RISC components so far characterized in human and Drosophila, as well as novel proteins involved in RNA metabolism. In agreement with its loading with heterochromatic small RNAs, Tg-AGO also associates substoichiometrically with components of known chromatin-repressing complexes. Thus, a puzzling patchwork of silencing processor and effector proteins from plant, fungal and metazoan origin accounts for the production and action of an unsuspected variety of small RNAs in the single-cell parasite Toxoplasma and possibly in other apicomplexans. This study establishes Toxoplasma as a unique model system for studying the evolution and molecular mechanisms of RNA silencing among eukaryotes. Toxoplasma gondii is an important human parasite that causes life-threatening diseases in developing fetuses and in immunocompromised individuals, especially AIDS and transplant patients. Curiously, the Toxoplasma genome is deprived of most of the basic transcription factors that regulate gene expression in other eukaryotic cells. Therefore, alternative strategies must exist to modulate the many phases of the Toxoplasma complex life cycle that includes invasion of several hosts. Here, we investigate one of these strategies, by studying the repertoire of Toxoplasma silencing small RNAs (sRNAs). In eukaryotes, most of these regulatory molecules, 20–30nt-long, are produced by members of the Dicer RNase-III family, and exert their various functions through ubiquitous proteins called Argonaute (Ago). The surprising diversity of the Toxoplasma sRNAome uncovered in our study is consistent with those molecules exerting key functions during the parasite's life cycle, including, possibly, during virulent infection. The study also unravels an unsuspected level of complexity in the origin and mechanisms of action of the factors that generate and affect Toxoplasma sRNA, prompting a re-evaluation of our current views on RNA silencing in eukaryotes.
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Affiliation(s)
- Laurence Braun
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163-ATIP+ group, Université Joseph Fourier, Grenoble, France
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32
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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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Baudet M, Ortet P, Gaillard JC, Fernandez B, Guérin P, Enjalbal C, Subra G, de Groot A, Barakat M, Dedieu A, Armengaud J. Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics 2009; 9:415-26. [PMID: 19875382 PMCID: PMC2830850 DOI: 10.1074/mcp.m900359-mcp200] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [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] [Indexed: 01/28/2023] Open
Abstract
Deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. To achieve a comprehensive and accurate annotation of the Deinococcus deserti genome, we performed an N terminus-oriented characterization of its proteome. For this, we used a labeling reagent, N-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein N termini. The large scale identification of N-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide-modified N-terminal-most peptides by shotgun liquid chromatography-tandem mass spectrometry analysis led to the validation of 278 and the correction of 73 translation initiation codons in the D. deserti genome. In addition, four new genes were detected, three located on the main chromosome and one on plasmid P3. We also analyzed signal peptide cleavages on a genome-wide scale. Based on comparative proteogenomics analysis, we propose a set of 137 corrections to improve Deinococcus radiodurans and Deinococcus geothermalis gene annotations. Some of these corrections affect important genes involved in DNA repair mechanisms such as polA, ligA, and ddrB. Surprisingly, experimental evidences were obtained indicating that DnaA (the protein involved in the DNA replication initiation process) and RpsL (the S12 ribosomal conserved protein) translation is initiated in Deinococcaceae from non-canonical codons (ATC and CTG, respectively). Such use may be the basis of specific regulation mechanisms affecting replication and translation. We also report the use of non-conventional translation initiation codons for two other genes: Deide_03051 and infC. Whether such use of non-canonical translation initiation codons is much more frequent than for other previously reported bacterial phyla or restricted to Deinococcaceae remains to be investigated. Our results demonstrate that predicting translation initiation codons is still difficult for some bacteria and that proteomics-based refinement of genome annotations may be helpful in such cases.
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Affiliation(s)
- Mathieu Baudet
- Laboratoire de Biochimie des Systèmes Perturbés, Service de Biochimie et Toxicologie Nucléaire, Institut de Biologie Environnementale et Biotechnologie (iBEB), Direction des Sciences du Vivant (DSV), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), F-30207 Bagnols-sur-Cèze, France
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Barakat M, Ortet P, Jourlin-Castelli C, Ansaldi M, Méjean V, Whitworth DE. P2CS: a two-component system resource for prokaryotic signal transduction research. BMC Genomics 2009; 10:315. [PMID: 19604365 PMCID: PMC2716373 DOI: 10.1186/1471-2164-10-315] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [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: 01/27/2009] [Accepted: 07/15/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the escalation of high throughput prokaryotic genome sequencing, there is an ever-increasing need for databases that characterise, catalogue and present data relating to particular gene sets and genomes/metagenomes. Two-component system (TCS) signal transduction pathways are the dominant mechanisms by which micro-organisms sense and respond to external as well as internal environmental changes. These systems respond to a wide range of stimuli by triggering diverse physiological adjustments, including alterations in gene expression, enzymatic reactions, or protein-protein interactions. DESCRIPTION We present P2CS (Prokaryotic 2-Component Systems), an integrated and comprehensive database of TCS signal transduction proteins, which contains a compilation of the TCS genes within 755 completely sequenced prokaryotic genomes and 39 metagenomes. P2CS provides detailed annotation of each TCS gene including family classification, sequence features, functional domains, as well as genomic context visualization. To bypass the generic problem of gene underestimation during genome annotation, we also constituted and searched an ORFeome, which improves the recovery of TCS proteins compared to searches on the equivalent proteomes. CONCLUSION P2CS has been developed for computational analysis of the modular TCSs of prokaryotic genomes and metagenomes. It provides a complete overview of information on TCSs, including predicted candidate proteins and probable proteins, which need further curation/validation. The database can be browsed and queried with a user-friendly web interface at http://www.p2cs.org/.
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Affiliation(s)
- Mohamed Barakat
- CEA, DSV, IBEB, LEMiRE, CNRS, Université Aix-Marseille II, CEA Cadarache, F-13108 Saint-Paul-lez-Durance, France.
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Bougdour A, Maubon D, Baldacci P, Ortet P, Bastien O, Bouillon A, Barale JC, Pelloux H, Ménard R, Hakimi MA. Drug inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites. ACTA ACUST UNITED AC 2009; 206:953-66. [PMID: 19349466 PMCID: PMC2715132 DOI: 10.1084/jem.20082826] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [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] [Indexed: 02/02/2023]
Abstract
Plasmodium and Toxoplasma are parasites of major medical importance that belong to the Apicomplexa phylum of protozoa. These parasites transform into various stages during their life cycle and express a specific set of proteins at each stage. Although little is yet known of how gene expression is controlled in Apicomplexa, histone modifications, particularly acetylation, are emerging as key regulators of parasite differentiation and stage conversion. We investigated the anti-Apicomplexa effect of FR235222, a histone deacetylase inhibitor (HDACi). We show that FR235222 is active against a variety of Apicomplexa genera, including Plasmodium and Toxoplasma, and is more potent than other HDACi's such as trichostatin A and the clinically relevant compound pyrimethamine. We identify T. gondii HDAC3 (TgHDAC3) as the target of FR235222 in Toxoplasma tachyzoites and demonstrate the crucial role of the conserved and Apicomplexa HDAC-specific residue TgHDAC3 T99 in the inhibitory activity of the drug. We also show that FR235222 induces differentiation of the tachyzoite (replicative) into the bradyzoite (nonreplicative) stage. Additionally, via its anti-TgHDAC3 activity, FR235222 influences the expression of ∼370 genes, a third of which are stage-specifically expressed. These results identify FR235222 as a potent HDACi of Apicomplexa, and establish HDAC3 as a central regulator of gene expression and stage conversion in Toxoplasma and, likely, other Apicomplexa.
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Affiliation(s)
- Alexandre Bougdour
- UMR, Centre National de la Recherche Scientifique, Université Joseph Fourier Grenoble, France
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Sautel CF, Ortet P, Saksouk N, Kieffer S, Garin J, Bastien O, Hakimi MA. The histone methylase KMTox interacts with the redox-sensor peroxiredoxin-1 and targets genes involved in Toxoplasma gondii antioxidant defences. Mol Microbiol 2008; 71:212-26. [PMID: 19017266 DOI: 10.1111/j.1365-2958.2008.06519.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ability of living cells to alter their gene expression patterns in response to environmental changes is essential for viability. Oxidative stress represents a common threat for all aerobic life. In normally growing cells, in which hydrogen peroxide generation is transient or pulsed, the antioxidant systems efficiently control its concentration. Intracellular parasites must also protect themselves against the oxidative burst imposed by the host. In this work, we have investigated the role of KMTox, a new histone lysine methyltransferase, in the obligate intracellular parasite Toxoplasma gondii. KMTox is a nuclear protein that holds a High Mobility Group domain, which is thought to recognize bent DNA. The enzyme methylates both histones H4 and H2A in vitro with a great preference for the substrate in reduced conditions. Importantly, KMTox interacts specifically with the typical 2-cys peroxiredoxin-1 and the binding is to some extent enhanced upon oxidation. It appears that the cellular functions that are primarily regulated by the KMTox are antioxidant defences and maintenance of cellular homeostasis. KMTox may regulate gene expression in T. gondii by providing the rapid re-arrangement of chromatin domains and by interacting with the redox-sensor TgPrx1 contribute to establish the antioxidant 'firewall' in T. gondii.
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Affiliation(s)
- Céline F Sautel
- Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier GRENOBLE 1, BP 170, F-38042 Grenoble cedex 9, France
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Hu GQ, Zheng X, Yang YF, Ortet P, She ZS, Zhu H. ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res 2007; 36:D114-9. [PMID: 17942412 PMCID: PMC2238952 DOI: 10.1093/nar/gkm799] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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] [Indexed: 11/30/2022] Open
Abstract
Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at http://mech.ctb.pku.edu.cn/protisa
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Affiliation(s)
- Gang-Qing Hu
- State Key Lab for Turbulence and Complex System and Department of Biomedical Engineering, Peking University, Beijing 100871, China
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Ricaud L, Proux C, Renou JP, Pichon O, Fochesato S, Ortet P, Montané MH. ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis. PLoS One 2007; 2:e430. [PMID: 17487278 PMCID: PMC1855986 DOI: 10.1371/journal.pone.0000430] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [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: 10/25/2006] [Accepted: 04/19/2007] [Indexed: 11/19/2022] Open
Abstract
ATM (Ataxia Telangiectasia Mutated) is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT). To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT) and homozygous ATM-deficient mutants challenged with a dose of γ-rays (IR) that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of prolonged S-G2 phases that coincided with cell proliferation delay, or an anticipated subsequent auxin increase, accelerated cell differentiation or death, was used to link IR-regulated hallmark functions and tissue phenotypes after IR. The transcription burst was almost exclusively AtATM-dependent or weakly AtATR-dependent, and followed two major trends of expression in atm: (i)-loss or severe attenuation and delay, and (ii)-inverse and/or stochastic, as well as specific, enabling one to distinguish IR/ATM pathway constituents. Our data provide a large resource for studies on the interaction between plant checkpoints of the cell cycle, development, hormone response, and DNA repair functions, because IR-induced transcriptional changes partially overlap with the response to environmental stress. Putative connections of ATM to stem cell maintenance pathways after IR are also discussed.
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Affiliation(s)
- Lilian Ricaud
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Caroline Proux
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Jean-Pierre Renou
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Olivier Pichon
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Sylvain Fochesato
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Philippe Ortet
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Marie-Hélène Montané
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
- * To whom correspondence should be addressed. E-mail:
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39
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Ricaud L, Proux C, Renou JP, Pichon O, Fochesato S, Ortet P, Montané MH. ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis. PLoS One 2007. [PMID: 17487278 DOI: 10.1371/.pone.0000430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
ATM (Ataxia Telangiectasia Mutated) is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT). To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT) and homozygous ATM-deficient mutants challenged with a dose of gamma-rays (IR) that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of prolonged S-G2 phases that coincided with cell proliferation delay, or an anticipated subsequent auxin increase, accelerated cell differentiation or death, was used to link IR-regulated hallmark functions and tissue phenotypes after IR. The transcription burst was almost exclusively AtATM-dependent or weakly AtATR-dependent, and followed two major trends of expression in atm: (i)-loss or severe attenuation and delay, and (ii)-inverse and/or stochastic, as well as specific, enabling one to distinguish IR/ATM pathway constituents. Our data provide a large resource for studies on the interaction between plant checkpoints of the cell cycle, development, hormone response, and DNA repair functions, because IR-induced transcriptional changes partially overlap with the response to environmental stress. Putative connections of ATM to stem cell maintenance pathways after IR are also discussed.
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Affiliation(s)
- Lilian Ricaud
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
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Muller D, Médigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsène-Ploetze F, Carapito C, Chandler M, Cournoyer B, Cruveiller S, Dossat C, Duval S, Heymann M, Leize E, Lieutaud A, Lièvremont D, Makita Y, Mangenot S, Nitschke W, Ortet P, Perdrial N, Schoepp B, Siguier P, Simeonova DD, Rouy Z, Segurens B, Turlin E, Vallenet D, Dorsselaer AV, Weiss S, Weissenbach J, Lett MC, Danchin A, Bertin PN. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet 2007; 3:e53. [PMID: 17432936 PMCID: PMC1851979 DOI: 10.1371/journal.pgen.0030053] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [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: 12/04/2006] [Accepted: 02/23/2007] [Indexed: 12/03/2022] Open
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. 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.
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Affiliation(s)
- Daniel Muller
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | | | - Sandrine Koechler
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | | | - Mohamed Barakat
- Laboratoire d'Écologie Microbienne de la Rhizosphère et d'Environnements Extrêmes, UMR6191 CNRS, CEA and Université Aix-Marseille II, Saint-Paul-lez-Durance, France
| | - Emmanuel Talla
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Evelyne Krin
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | - Florence Arsène-Ploetze
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Michael Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100 CNRS, Toulouse, France
| | - Benoît Cournoyer
- Ecologie Microbienne, UMR5557 CNRS and Université Claude Bernard–Lyon 1, Villeurbanne, France
| | | | | | - Simon Duval
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR9036 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Michael Heymann
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Emmanuelle Leize
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Aurélie Lieutaud
- Laboratoire de Chimie Bactérienne, UPR9043 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Didier Lièvremont
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Yuko Makita
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | | | - Wolfgang Nitschke
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR9036 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Philippe Ortet
- Laboratoire d'Écologie Microbienne de la Rhizosphère et d'Environnements Extrêmes, UMR6191 CNRS, CEA and Université Aix-Marseille II, Saint-Paul-lez-Durance, France
| | - Nicolas Perdrial
- Centre de Géochimie de la Surface, UMR7517 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Barbara Schoepp
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR9036 CNRS, Institut de Biologie Structurale et Microbiologie, Marseille, France
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100 CNRS, Toulouse, France
| | - Diliana D Simeonova
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Zoé Rouy
- Génoscope, UMR8030 CNRS, Evry Cedex, France
| | | | - Evelyne Turlin
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | | | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Stéphanie Weiss
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | | | - Marie-Claire Lett
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
| | - Antoine Danchin
- Génétique des Génomes Bactériens, URA2171, Institut Pasteur, Paris, France
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
- * To whom correspondence should be addressed. E-mail:
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Misson J, Raghothama KG, Jain A, Jouhet J, Block MA, Bligny R, Ortet P, Creff A, Somerville S, Rolland N, Doumas P, Nacry P, Herrerra-Estrella L, Nussaume L, Thibaud MC. A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc Natl Acad Sci U S A 2005; 102:11934-9. [PMID: 16085708 PMCID: PMC1188001 DOI: 10.1073/pnas.0505266102] [Citation(s) in RCA: 590] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphorus, one of the essential elements for plants, is often a limiting nutrient because of its low availability and mobility in soils. Significant changes in plant morphology and biochemical processes are associated with phosphate (Pi) deficiency. However, the molecular bases of these responses to Pi deficiency are not thoroughly elucidated. Therefore, a comprehensive survey of global gene expression in response to Pi deprivation was done by using Arabidopsis thaliana whole genome Affymetrix gene chip (ATH1) to quantify the spatio-temporal variations in transcript abundance of 22,810 genes. The analysis revealed a coordinated induction and suppression of 612 and 254 Pi-responsive genes, respectively. The functional classification of some of these genes indicated their involvement in various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. This study is a detailed analysis of Pi starvation-induced changes in gene expression of the entire genome of Arabidopsis correlated with biochemical processes. The results not only enhance our knowledge about molecular processes associated with Pi deficiency, but also facilitate the identification of key molecular determinants for improving Pi use by crop species.
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Affiliation(s)
- Julie Misson
- Laboratoire de Biologie du Développement des Plantes, Unite Mixte de Recherche 6191, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique, Aix-Marseille II, 13108 Saint-Paul-lez-Durance, France
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