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1. A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa.

Author

Jean-François Humbert, Valérie Barbe, Amel Latifi, Muriel Gugger, Alexandra Calteau, Therese Coursin, Aurélie Lajus, Vanina Castelli, Sophie Oztas, Gaëlle Samson, Cyrille Longin, Claudine Medigue, and Nicole Tandeau de Marsac

Subjects
Medicine, Science
Abstract

Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including three new putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.

Published
2013
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2. Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

Author

Philipp Engel, Walter Salzburger, Marius Liesch, Chao-Chin Chang, Soichi Maruyama, Christa Lanz, Alexandra Calteau, Aurélie Lajus, Claudine Médigue, Stephan C Schuster, and Christoph Dehio

Subjects
Genetics, QH426-470
Abstract

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment.

Published
2011
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3. Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles.

Author

Benoît Remenant, Jean-Charles de Cambiaire, Gilles Cellier, Jonathan M Jacobs, Sophie Mangenot, Valérie Barbe, Aurélie Lajus, David Vallenet, Claudine Medigue, Mark Fegan, Caitilyn Allen, and Philippe Prior

Subjects
Medicine, Science
Abstract

The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer.

Published
2011
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4. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

Author

Stéphane Vuilleumier, Ludmila Chistoserdova, Ming-Chun Lee, Françoise Bringel, Aurélie Lajus, Yang Zhou, Benjamin Gourion, Valérie Barbe, Jean Chang, Stéphane Cruveiller, Carole Dossat, Will Gillett, Christelle Gruffaz, Eric Haugen, Edith Hourcade, Ruth Levy, Sophie Mangenot, Emilie Muller, Thierry Nadalig, Marco Pagni, Christian Penny, Rémi Peyraud, David G Robinson, David Roche, Zoé Rouy, Channakhone Saenampechek, Grégory Salvignol, David Vallenet, Zaining Wu, Christopher J Marx, Julia A Vorholt, Maynard V Olson, Rajinder Kaul, Jean Weissenbach, Claudine Médigue, and Mary E Lidstrom

Subjects
Medicine, Science
Abstract

BACKGROUND:Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. METHODOLOGY/PRINCIPAL FINDINGS:The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). CONCLUSION/SIGNIFICANCE:These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.

Published
2009
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5. Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis.

Author

Mathieu Picardeau, Dieter M Bulach, Christiane Bouchier, Richard L Zuerner, Nora Zidane, Peter J Wilson, Sophie Creno, Elizabeth S Kuczek, Simona Bommezzadri, John C Davis, Annette McGrath, Matthew J Johnson, Caroline Boursaux-Eude, Torsten Seemann, Zoé Rouy, Ross L Coppel, Julian I Rood, Aurélie Lajus, John K Davies, Claudine Médigue, and Ben Adler

Subjects
Medicine, Science
Abstract

Leptospira biflexa is a free-living saprophytic spirochete present in aquatic environments. We determined the genome sequence of L. biflexa, making it the first saprophytic Leptospira to be sequenced. The L. biflexa genome has 3,590 protein-coding genes distributed across three circular replicons: the major 3,604 chromosome, a smaller 278-kb replicon that also carries essential genes, and a third 74-kb replicon. Comparative sequence analysis provides evidence that L. biflexa is an excellent model for the study of Leptospira evolution; we conclude that 2052 genes (61%) represent a progenitor genome that existed before divergence of pathogenic and saprophytic Leptospira species. Comparisons of the L. biflexa genome with two pathogenic Leptospira species reveal several major findings. Nearly one-third of the L. biflexa genes are absent in pathogenic Leptospira. We suggest that once incorporated into the L. biflexa genome, laterally transferred DNA undergoes minimal rearrangement due to physical restrictions imposed by high gene density and limited presence of transposable elements. In contrast, the genomes of pathogenic Leptospira species undergo frequent rearrangements, often involving recombination between insertion sequences. Identification of genes common to the two pathogenic species, L. borgpetersenii and L. interrogans, but absent in L. biflexa, is consistent with a role for these genes in pathogenesis. Differences in environmental sensing capacities of L. biflexa, L. borgpetersenii, and L. interrogans suggest a model which postulates that loss of signal transduction functions in L. borgpetersenii has impaired its survival outside a mammalian host, whereas L. interrogans has retained environmental sensory functions that facilitate disease transmission through water.

Published
2008
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6. MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.

Author

David Vallenet, Alexandra Calteau, Mathieu Dubois, Paul Amours, Adelme Bazin, Mylène Beuvin, Laura Burlot, Xavier Bussell, Stéphanie Fouteau, Guillaume Gautreau, Aurélie Lajus, Jordan Langlois, Rémi Planel, David Roche, Johan Rollin, Zoé Rouy, Valentin Sabatet, and Claudine Médigue

Published
2020
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12. MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

Author

Johan Rollin, Mathieu Gachet, Adrien Josso, Rémi Planel, Guillaume Gautreau, Hugo Pereira, David Roche, Alexandra Calteau, Jordan Langlois, Zoé Rouy, Claudine Médigue, David Vallenet, Stéphane Cruveiller, Aurélie Lajus, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Service d'Ecologie Sociale, CP 231, Universite´ Libre de Bruxelles, Boulevard du Triomphe, 1050 Brussels, Belgium, Université libre de Bruxelles (ULB), Représenter, Inventer la Réalité, du Romantisme au XXIe siècle (RIRRA 21), Université Paul-Valéry - Montpellier 3 (UPVM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE)

Subjects
0301 basic medicine, Paper, Computer science, Data management, Context (language use), Bacterial genome size, Computational biology, comparative genomics, Genome, 03 medical and health sciences, Annotation, transcriptomics, User-Computer Interface, microbial genome annotation system, Computer Graphics, Relevance (information retrieval), Molecular Biology, ComputingMilieux_MISCELLANEOUS, variant detection, Comparative genomics, Microbiological Phenomena, Internet, 030102 biochemistry & molecular biology, business.industry, Computational Biology, Molecular Sequence Annotation, Genome project, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genome, Microbial, 030104 developmental biology, ComputingMethodologies_PATTERNRECOGNITION, metabolic networks, Database Management Systems, business, gene function curation, Databases, Chemical, Metabolic Networks and Pathways, Software, Information Systems
Abstract

The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.

Published
2017

13. MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

Author

Stéphane Cruveiller, Zoé Rouy, Claude Scarpelli, David Roche, David Vallenet, Jonathan Mercier, Alexandre Renaux, Claudine Médigue, Johan Rollin, Adrien Josso, Mathieu Gachet, Alexandra Calteau, Aurélie Lajus, Informatics and Applied Informatics, and Faculty of Sciences and Bioengineering Sciences

Subjects
0301 basic medicine, Data management, 030106 microbiology, Context (language use), Biology, Polymorphism, Single Nucleotide, Genome, Evolution, Molecular, 03 medical and health sciences, Consistency (database systems), Annotation, Databases, Genetic, Genetics, Database Issue, Metabolomics, Biological data, Ecology, business.industry, Microbiota, Computational Biology, Genome project, Data science, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Metagenomics, Multigene Family, Metabolome, Metagenome, business, Software
Abstract

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations.

Published
2016

14. Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21

Author

Zoé Rouy, Christelle Gruffaz, Pauline Chaignaud, Emilie E. L. Muller, Bruno Maucourt, Muhammad Farhan Ul Haque, Dick B. Janssen, Aurélie Lajus, Christiaan P. Postema, Françoise Bringel, Louis Hermon, Thierry Nadalig, Sophie Mangenot, Stéphane Vuilleumier, Sabrina Bibi-Triki, Yousra Louhichi, Claudine Médigue, Valérie Barbe, Biotechnology, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Laboratoire Hétéroéléments et Coordination (DCPH), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), UMR7156 Génétique moléculaire, génomique et microbiologie (GMGM), Université de Strasbourg (UNISTRA), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE)

Subjects
0301 basic medicine, Whole genome sequencing, inorganic chemicals, Strain (chemistry), Biology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, Biochemistry, chemistry, 13. Climate action, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Journal Article, Prokaryotes, Hyphomicrobium sp, Energy source, Molecular Biology, Bacteria, ComputingMilieux_MISCELLANEOUS, Dichloromethane
Abstract

The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples of environments contaminated with halogenated pollutants and capable of using dichloromethane as its sole carbon and energy source, was determined.

Published
2017

15. The genomic and transcriptomic basis of the potential of Lactobacillus plantarum A6 to improve the nutritional quality of a cereal based fermented food

Author

Williams Turpin, Marion Weiman, Aurélie Lajus, Stéphane Cruveiller, Christèle Humblot, and Jean-Pierre Guyot

Subjects
0301 basic medicine, Pennisetum, 030106 microbiology, Genomics, Biology, Carbohydrate metabolism, Microbiology, Genome, DNA sequencing, Transcriptome, 03 medical and health sciences, Lactobacillus, Gene, food and beverages, High-Throughput Nucleotide Sequencing, General Medicine, biology.organism_classification, 030104 developmental biology, Biochemistry, Food Microbiology, Carbohydrate Metabolism, Fermented Foods, Edible Grain, Nutritive Value, Lactobacillus plantarum, Genome, Bacterial, Food Science
Abstract

The objective of this work was to investigate the nutritional potential of Lactobacillus plantarum A6 in a food matrix using next generation sequencing. To this end, we characterized the genome of the A6 strain for a complete overview of its potential. We then compared its transcriptome when grown in a food matrix made from pearl millet to and its transcriptome when cultivated in a laboratory medium. Genomic comparison of the strain L. plantarum A6 with the strains WCFS1, ST-III, JDM1 and ATCC14917 led to the identification of five regions of genomic plasticity. More specifically, 362 coding sequences, mostly annotated as coding for proteins of unknown functions, were specific to L. plantarum A6. A total of 1201 genes were significantly differentially expressed in laboratory medium and food matrix. Among them, 821 genes were up-regulated in the food matrix compared to the laboratory medium, representing 23% of whole genomic objects. In the laboratory medium, the expression of 380 genes, representing 11% of the all genomic objects was at least double than in the food matrix. Genes encoding important functions for the nutritional quality of the food were identified. Considering its efficiency as an amylolytic strain, we investigated all genes involved in carbohydrate metabolism, paying particular attention to starch metabolism. An extracellular alpha amylase, a neopullulanase and maltodextrin transporters were identified, all of which were highly expressed in the food matrix. In addition, genes involved in alpha-galactoside metabolism were identified but only two of them were induced in food matrix than in laboratory medium. This may be because alpha galactosides were already eliminated during soaking. Different biosynthetic pathways involved in the synthesis of vitamin B (folate, riboflavin, and cobalamin) were identified. They allowed the identification of a potential of vitamin synthesis, which should be confirmed through biochemical analysis in further work. Surprisingly, some genes involved in metabolism and bioaccessibility of iron were identified. They were related directly to the use of transport of iron, or indirectly to metabolism of polyphenols, responsible of iron chelation in the food. The combination of genomics and transcriptomics not only revealed previously undocumented nutritional properties of L. plantarum A6, but also documented the behaviour of this bacterium in food.

Published
2017

16. Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain

Author

Laurent Marché, Catherine Cailliez-Grimal, Benoit Remenant, Frédéric Borges, Monique Zagorec, Aurélie Lajus, Hervé Prévost, Anne-Marie Revol-Junelles, Marie-France Pilet, Claudine Médigue, SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Laboratoire d'Ingénierie des Biomolécules (LIBio), Université de Lorraine (UL), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Sécurité des Aliments (SECALIM), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Nantes, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Ecole Nationale Vétérinaire de Nantes-Institut National de la Recherche Agronomique (INRA), Institut de Biologie François JACOB (JACOB), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay

Subjects
0301 basic medicine, bactérie lactique, [SDV]Life Sciences [q-bio], 030106 microbiology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Genome, lignée divergente, bacteriocine, 03 medical and health sciences, Polyketide, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Bacteriocin, polyketide, Genetics, Prokaryotes, caractérisation souche bactérienne, Molecular Biology, Gene, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Strain (chemistry), carnobacterium divergens, séquence génomique, biology.organism_classification, Biopreservation, 030104 developmental biology, conservation biologique, Bacteria, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

In this study, we present the draft genome sequence of Carnobacterium divergens V41. This strain was previously reported as producing divercin V41, a bacteriocin of interest for food biopreservation. Its genome revealed also the presence of a gene cluster putatively involved in polyketide production, which is unique in lactic acid bacteria.

Published
2016

17. MaGe: a microbial genome annotation system supported by synteny results

Author

Claude Scarpelli, Zoé Rouy, David Vallenet, Laurent Labarre, Stéphanie Bocs, Stéphane Cruveiller, Claudine Médigue, Valérie Barbe, Géraldine Pascal, Aurélie Lajus, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
endocrine system, Biological database, Genomics, Bacterial genome size, Vertebrate and Genome Annotation Project, Biology, Synteny, Genome, Article, User-Computer Interface, 03 medical and health sciences, Annotation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Databases, Genetic, Computer Graphics, Genetics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Internet, 0303 health sciences, 030306 microbiology, Computational Biology, Genome project, Systems Integration, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Database Management Systems, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial
Abstract

Magnifying Genomes (MaGe) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. Our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions. MaGe is also linked to numerous well-known biological databases and systems. Our system has been thoroughly tested during the annotation of complete bacterial genomes (Acinetobacter baylyi ADP1, Pseudoalteromonas haloplanktis, Frankia alni) and is currently used in the context of several new microbial genome annotation projects. In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage.

Published
2006

18. MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes

Author

Jérôme Le Saux, Aurélie Lajus, Stéphane Cruveiller, David Vallenet, Claudine Médigue, and Stéphanie Bocs

Subjects
Genetics, Internet, Time Factors, Reproducibility of Results, Genomics, Context (language use), Bacterial genome size, Gene Annotation, Computational biology, Vertebrate and Genome Annotation Project, Biology, Article, User-Computer Interface, Annotation, ComputingMethodologies_PATTERNRECOGNITION, Genes, Bacterial, Computer Graphics, RefSeq, Databases, Nucleic Acid, Genome, Bacterial, Software, Reference genome
Abstract

The annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. DNA sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. This first annotation step is generally followed by an expert manual annotation of the predicted genes. The genomic data (sequence and annotations) organized in an appropriate databank file format is subsequently submitted to an entry point of the International Nucleotide Sequence Database. These procedures are inevitably subject to mistakes, and this can lead to unintentional syntactic annotation errors being stored in public databanks. Here, we present a new web program, MICheck (MIcrobial genome Checker), that enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes. The web interface allows one easily to investigate the MICheck results, i.e. inaccurate or missed gene annotations: a graphical representation is drawn, in which the genomic context of a unique coding DNA sequence annotation or a predicted frameshift is given, using information on the coding potential (curves) and annotation of the neighbouring genes. We illustrate some capabilities of the MICheck site through the analysis of 20 bacterial genomes, 9 of which were selected for their 'Reviewed' status in the National Center for Biotechnology Information (NCBI) Reference Sequence Project (RefSeq). In the context of the numerous re-annotation projects for microbial genomes, this tool can be seen as a preliminary step before the functional re-annotation step to check quickly for missing or wrongly annotated genes. The MICheck website is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/micheck.

Published
2005

19. Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8

Author

Mike S. M. Jetten, Ahmet Zeytun, J. Colin Murrell, Lynne Goodwin, K. Dimitri Kits, Alex Copeland, Loren Hauser, Samuel Pitluck, Françoise Bringel, Susan Lucas, Huub J. M. Op den Camp, Alla Lapidus, David Bruce, Marina G. Kalyuzhnaya, Aurélie Lajus, Claudine Médigue, Martin G. Klotz, Jan Fang Cheng, Miriam Land, Lisa Y. Stein, Stéphane Vuilleumier, Alan A. DiSpirito, Tanja Woyke, University of Alberta, University of Washington [Seattle], University of North Carolina [Charlotte] (UNC), University of North Carolina System (UNC), Department of Aquatic Ecology & Environmental Biology, Radboud University [Nijmegen], Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Iowa State University (ISU), School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Los Alamos National Laboratory (LANL), DOE Joint Genome Institute [Walnut Creek], Department of Energy / Joint Genome Institute (DOE), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Groupe d'Etudes des Matériaux Hétérogènes (GEMH), Université de Limoges (UNILIM)-Institut des Procédés Appliqués aux Matériaux (IPAM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Department of Molecular and Cell Biology, University of Connecticut (UCONN), Radboud university [Nijmegen], and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
Whole genome sequencing, 0303 health sciences, Obligate, Methanotroph, 030306 microbiology, Strain (biology), Biology, 03 medical and health sciences, Fixation (population genetics), Ecological Microbiology, Botany, Genetics, Methylomicrobium album, Prokaryotes, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Molecular Biology, Gene, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, 030304 developmental biology
Abstract

The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N fixation.

Published
2013

20. Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies

Author

Peter Tiffin, Michael J. Sadowsky, Jimmy E. Woodward, Arvind K. Bharti, Aurélie Lajus, David Vallenet, Prasad Gyaneshwar, Andrew Farmer, Brian D. Badgley, Masayuki Sugawara, Zoé Rouy, Brendan Epstein, Jennifer Reese, Roxanne Denny, Tatsuya Unno, Betsy M. Martinez-Vaz, Lei Xu, Claudine Médigue, Gregory D. May, Joann Mudge, and Nevin D. Young

Subjects
Lipopolysaccharides, Comparative genomics, Genetics, 0303 health sciences, Sinorhizobium meliloti, Medicago, 030306 microbiology, Research, food and beverages, Sinorhizobium, Biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Genome, Nod factor, 03 medical and health sciences, Nitrogen Fixation, Nitrogen fixation, Symbiosis, Bacterial Secretion Systems, Genome, Bacterial, Phylogeny, 030304 developmental biology, Sulfur utilization
Abstract

Background The sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group. Results Here we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content, including those involved in conjugation and organic sulfur utilization. Genes involved in Nod factor and polysaccharide biosynthesis, denitrification and type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency. Conclusions Our results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. The diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.

Published
2013

21. A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa

Author

Nicole Tandeau de Marsac, Sophie Oztas, Jean-François Humbert, Valérie Barbe, Vanina Castelli, Alexandra Calteau, Gaëlle Samson, Aurélie Lajus, Thérèse Coursin, Muriel Gugger, Amel Latifi, Cyrille Longin, Claudine Médigue, Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Collection des Cyanobactéries, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
atlantic ocean, microcystis aeruginosa, Fresh Water, Genome, Genome Size, Gene Order, Genome Sequencing, Phylogeny, Genetics, 0303 health sciences, Base Composition, Multidisciplinary, biology, marine cyanobacteria, Genomics, genetic diversity, toxic cyanobacterium, Multigene Family, Medicine, Prochlorococcus, ecology, Water Microbiology, Research Article, Genome evolution, Microcystis, Gene Transfer, Horizontal, Science, cyanobactérie, prochlorococcus, nonribosomal peptide synthetase, evolution, populations, biosynthesis, Microbiology, Microbial Ecology, 03 medical and health sciences, Microcystis aeruginosa, 14. Life underwater, Genome size, Biology, Ecosystem, 030304 developmental biology, Repetitive Sequences, Nucleic Acid, Comparative genomics, Evolutionary Biology, 030306 microbiology, Computational Biology, Bacteriology, Comparative Genomics, biology.organism_classification, Evolutionary Ecology, Microbial Evolution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, GC-content, Genome, Bacterial
Abstract

International audience; Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including threenew putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.

Published
2013

22. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

Author

Eugeni Belda, Cyrille Longin, Stefan Engelen, David Vallenet, Adam Alexander T. Smith, Stéphane Cruveiller, Gregory Salvignol, David Roche, Claude Scarpelli, Aurélie Lajus, Zoé Rouy, Claudine Médigue, Alexandra Calteau, François Le Fèvre, Damien Mornico, and Marion Weiman

Subjects
Context (language use), Genomics, Biology, Genome, Synteny, World Wide Web, Evolution, Molecular, 03 medical and health sciences, Annotation, Resource (project management), Genome, Archaeal, Databases, Genetic, Genetics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Internet, Data curation, Bacteria, 030306 microbiology, Gene Expression Profiling, Gene Annotation, Genome project, Articles, Enzymes, Systems Integration, ComputingMethodologies_PATTERNRECOGNITION, Genome, Bacterial, Metabolic Networks and Pathways, Software
Abstract

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest.

Published
2012

23. Complete Genome Sequences of Six Strains of the Genus Methylobacterium

Author

Tanja Woyke, Rémi Peyraud, Muhammad Farhan Ul Haque, Julia A. Vorholt, Lynne Goodwin, Françoise Bringel, Claudine Médigue, Thierry Nadalig, Matt Nolan, Ming-Chun Lee, Emilie E. L. Muller, Lionel Moulin, Christelle Gruffaz, Philippe Jourand, Aurélie Lajus, Claudia Knief, Natalia Mikhailova, Lina Russ, Ludmila Chistoserdova, Stéphane Vuilleumier, Sergey Stolyar, Miriam Land, Sandro Roselli, Nikos C. Kyrpides, Christopher J. Marx, Natalia Ivanova, Darrell E. Fleischman, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), EWHA Womans University (EWHA), Laboratoire d'automatique et de génie des procédés (LAGEP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, MESH: Sequence Analysis, DNA, Sequence analysis, Molecular Sequence Data, MESH: Base Sequence, MESH: Genome, Bacterial, Microbiology, Genome, 03 medical and health sciences, Base sequence, Molecular Biology, 030304 developmental biology, Genetics, 0303 health sciences, MESH: Molecular Sequence Data, biology, Base Sequence, 030306 microbiology, Bacterial, Chromosome Mapping, DNA, Sequence Analysis, DNA, biology.organism_classification, MESH: DNA, Bacterial, Genome Announcements, Methylobacterium, bacteria, MESH: Chromosome Mapping, Genus Methylobacterium, Sequence Analysis, Genome, Bacterial, MESH: Methylobacterium, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; The complete and assembled genome sequences were determined for six strains of the alphaproteobacterial genus Methylobacterium, chosen for their key adaptations to different plant-associated niches and environmental constraints.

Published
2012

24. Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius

Author

David Vallenet, Aurélie Lajus, Martha E. Trujillo, Philippe Normand, Lorena Carro, Pedro M. Coll, Pablo Alonso-Vega, Petar Pujic, Rodrigo Bacigalupe, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
DNA, Bacterial, Root nodule, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, Microbiology, Micromonospora lupini, Micromonospora, 03 medical and health sciences, Lupinus, Botany, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Legume, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Nucleic acid sequence, Sequence Analysis, DNA, respiratory system, biology.organism_classification, Genome Announcements, Lupinus angustifolius, Micromonosporaceae, Root Nodules, Plant, human activities, Genome, Bacterial
Abstract

Micromonospora strains have been isolated from diverse niches, including soil, water, and marine sediments and root nodules of diverse symbiotic plants. In this work, we report the genome sequence of Micromonospora lupini Lupac 08 isolated from root nodules of the wild legume Lupinus angustifolious .

Published
2012

25. Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z

Author

Françoise Bringel, Mike S. M. Jetten, Huub J. M. Op den Camp, Alexandr S. Reshetnikov, Jeremy D. Semrau, Yuri A. Trotsenko, Peter F. Dunfield, Claudine Médigue, Stéphane Vuilleumier, Valérie Barbe, Valentina N. Khmelenina, Martin G. Klotz, Zoé Rouy, Alan A. DiSpirito, Sophie Mangenot, Aurélie Lajus, Lisa Y. Stein, Marina G. Kalyuzhnaya, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Skryabin Institute of biochemistry and physiology of microorganisms (IBPM/RAS), Russian Academy of Sciences [Moscow] (RAS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Alberta, Skryabin Institute of Biochemistry and Physiology of Microorganisms (IBPM/RAS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay

Subjects
Molecular Sequence Data, MESH: Genome, Bacterial, Microbiology, 03 medical and health sciences, Plasmid, MESH: Plasmids, Gammaproteobacteria, Molecular Biology, 030304 developmental biology, Genetics, Whole genome sequencing, 0303 health sciences, Methylomicrobium alcaliphilum, MESH: Molecular Sequence Data, biology, 030306 microbiology, biology.organism_classification, Genome Announcements, MESH: Gammaproteobacteria, Ecological Microbiology, Methanotrophic bacterium, Genome, Bacterial, Bacteria, Plasmids, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported.

Published
2012

26. Complete genome sequence of the chloromethane-degrading Hyphomicrobium sp. strain MC1

Author

Françoise Bringel, Emilie E. L. Muller, Aurélie Lajus, Stéphane Vuilleumier, Ghislaine Magdelenat, Muhammad Farhan Ul Haque, Thierry Nadalig, Valérie Barbe, Claudine Médigue, Sandro Roselli, Christelle Gruffaz, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Neurobiologie et Développement (N&eD), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, MESH: Sequence Analysis, DNA, food.ingredient, Molecular Sequence Data, Industrial Waste, MESH: Carbon, MESH: Genome, Bacterial, Microbiology, Genome, 03 medical and health sciences, chemistry.chemical_compound, food, MESH: Aerobiosis, MESH: Industrial Waste, Molecular Biology, MESH: Sewage, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, MESH: Molecular Sequence Data, biology, Strain (chemistry), Sewage, 030306 microbiology, Chloromethane, MESH: Methyl Chloride, Sequence Analysis, DNA, biology.organism_classification, Hyphomicrobium, MESH: DNA, Bacterial, Aerobiosis, Carbon, 3. Good health, Genome Announcements, Biochemistry, chemistry, Methyl Chloride, Methylotroph, Energy source, MESH: Hyphomicrobium, Bacteria, Genome, Bacterial, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Hyphomicrobium sp. strain MC1 is an aerobic methylotroph originally isolated from industrial sewage. This prosthecate bacterium was the first strain reported to grow with chloromethane as the sole carbon and energy source. Its genome, consisting of a single 4.76-Mb chromosome, is the first for a chloromethane-degrading bacterium to be formally reported.

Published
2011

27. Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales

Author

Françoise Bringel, Roger E. Bumgarner, Nicole E. Smalley, Weerayuth Kittichotirat, Claudine Médigue, Stéphane Vuilleumier, David A. C. Beck, Aurélie Lajus, Rob Hall, Marina G. Kalyuzhnaya, Nathan Good, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, MESH: Oxidation-Reduction, MESH: Signal Transduction, Geologic Sediments, MESH: Sequence Analysis, DNA, Molecular Sequence Data, Rhodocyclaceae, MESH: Genome, Bacterial, Microbiology, 03 medical and health sciences, Methyloversatilis universalis, MESH: Rhodocyclaceae, MESH: Phylogeny, Molecular Biology, Phylogeny, 030304 developmental biology, Genetics, Whole genome sequencing, 0303 health sciences, MESH: Molecular Sequence Data, biology, 030306 microbiology, Order Rhodocyclales, Sequence Analysis, DNA, MESH: Geologic Sediments, biology.organism_classification, Methyloversatilis, MESH: DNA, Bacterial, Genome Announcements, Multigene Family, Pure culture, MESH: Multigene Family, Oxidation-Reduction, Genome, Bacterial, Bacteria, Signal Transduction, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Rhodocyclales are representative of versatile bacteria that are able to utilize a wide variety of organic compounds for growth, but only a few strains have been isolated in pure culture thus far. Here we present the genome sequence of Methyloversatilis universalis FAM5 T , the first cultivable methylotrophic member of the order.

Published
2011

28. Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96

Author

Stéphane Vuilleumier, Sam Pitluck, Claudine Médigue, Susan Lucas, Matt Nolan, Alla Lapidus, David Bruce, Cliff Han, Mette M. Svenning, Loren Hauser, James Han, Lisa Y. Stein, Lynne Goodwin, Brittany Held, Anne Grethe Hestnes, Natalia Ivanova, Jan Fang Cheng, Françoise Bringel, Marina G. Kalyuzhnaya, Martin G. Klotz, Miriam Land, Tanja Woyke, Ingvild Wartiainen, Anja Spang, Aurélie Lajus, University of Alberta, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
Methanotroph, Molecular Sequence Data, medicine.disease_cause, Microbiology, Methylococcaceae, Genome, 03 medical and health sciences, Botany, medicine, Molecular Biology, Soil Microbiology, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, biology, Base Sequence, 030306 microbiology, Arctic Regions, Methylobacter tundripaludum, biology.organism_classification, Genome Announcements, Arctic, Nitrogen fixation, Soil microbiology, Methane, Genome, Bacterial, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Methylobacter tundripaludum SV96 T (ATCC BAA-1195) is a psychrotolerant aerobic methane-oxidizing gammaproteobacterium ( Methylococcales , Methylococcaceae ) living in High Arctic wetland soil. The strain was isolated from soil harvested in July 1996 close to the settlement Ny-Ålesund, Svalbard, Norway (78°56′N, 11°53′E), and described as a novel species in 2006. The genome includes pmo and pxm operons encoding copper membrane monooxygenases (Cu-MMOs), genes required for nitrogen fixation, and the nirS gene implicated in dissimilatory nitrite reduction to NO but no identifiable inventory for further processing of nitrogen oxides. These genome data provide the basis to investigate M. tundripaludum SV96, identified as a major player in the biogeochemistry of Arctic environments.

Published
2011

29. Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles

Author

Philippe Prior, Claudine Médigue, Benoit Remenant, Jean-Charles de Cambiaire, Caitilyn Allen, David Vallenet, Jonathan M. Jacobs, Gilles Cellier, Aurélie Lajus, Valérie Barbe, Sophie Mangenot, and Mark Fegan

Subjects
Asia, Science, Molecular Sequence Data, Pathogenesis, Ralstonia, Microbiology, Microbial Ecology, Plant Microbiology, Species Specificity, Phylogenetics, Biology, Genome Evolution, Ralstonia syzygii, Phylogeny, Phylotype, Comparative genomics, Ralstonia solanacearum, Multidisciplinary, Phylogenetic tree, biology, Base Sequence, food and beverages, Genomics, Sequence Analysis, DNA, Comparative Genomics, biology.organism_classification, Bacterial Pathogens, Genes, Bacterial, Horizontal gene transfer, Microbial Evolution, Medicine, Genome, Bacterial, Research Article
Abstract

The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer.

Published
2011

30. Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella

Author

Chao-Chin Chang, Soichi Maruyama, Stephan C. Schuster, Alexandra Calteau, Christoph Dehio, Marius Liesch, Walter Salzburger, Aurélie Lajus, Philipp Engel, Christa Lanz, Claudine Médigue, University of Zurich, and Dehio, Christoph

Subjects
Cancer Research, Adaptation, Biological, Infectious Diseases/Bacterial Infections, SX00 SystemsX.ch, 1306 Cancer Research, Evolutionary Biology/Genomics, SX06 InfectX, Bacterial Secretion Systems, Phylogeny, Genetics (clinical), 0303 health sciences, Microbiology/Microbial Evolution and Genomics, biology, Effector, Genetics and Genomics/Microbial Evolution and Genomics, Biological Evolution, Infectious Diseases, Evolutionary Biology/Microbial Evolution and Genomics, Host-Pathogen Interactions, Genetics and Genomics/Comparative Genomics, Bartonella, Research Article, 2716 Genetics (clinical), lcsh:QH426-470, Genetic Speciation, Molecular Biology/Molecular Evolution, Microbiology, 03 medical and health sciences, Bacterial Proteins, 1311 Genetics, Molecular evolution, Phylogenetics, Genetics, 1312 Molecular Biology, Animals, Humans, Genetics and Genomics/Genomics, Selection, Genetic, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Key innovation, Evolutionary Biology/Evolutionary and Comparative Genetics, 030306 microbiology, Human evolutionary genetics, Computational Biology, Genetics and Genomics, Molecular Sequence Annotation, Sequence Analysis, DNA, biology.organism_classification, Rats, Evolvability, lcsh:Genetics, Genetics and Genomics/Genome Projects, HEK293 Cells, 1105 Ecology, Evolution, Behavior and Systematics, Evolutionary biology, 570 Life sciences, Adaptation
Abstract

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment., Author Summary Adaptive radiation is the rapid origination of an array of species by the divergent colonization of disparate ecological niches. In the case of pathogenic bacteria, radiations can lead to the emergence of novel human pathogens. Being divergently adapted to a range of different mammalian hosts, including humans as reservoir or incidental hosts, the genus Bartonella represents a suitable model to study genomic mechanisms underpinning divergent adaptation of pathogens. Here we show that two distinct lineages of Bartonella have radiated in parallel, resulting in two arrays of evolutionary distinct species adapted to overlapping sets of mammalian hosts. Such parallelisms display excellent models to reveal insights into the genetic mechanisms underlying these independent evolutionary processes. Our genome-wide analysis identifies a striking evolutionary parallelism in a horizontally-acquired protein secretion system in the two lineages. The parallel evolutionary trajectory of this system in the two lineages is characterized by the convergent origination of a wide array of adaptive functions dedicated to the cellular interaction within the mammalian hosts. The parallel evolution of the two radiating lineages on the ecological as well as on the molecular level suggests that the horizontal acquisition and the functional diversification of the secretion system display an evolutionary key innovation underlying adaptive evolution.

Published
2011

31. From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma

Author

Francis Mégraud, Christiane Bouchier, Anne Ruskoné-Foumestraux, Zoé Rouy, Ivo G. Boneca, Sophie Creno, Dominique Lamarque, Marie-Agnès Dillies, Caroline Boursaux-Eude, Claudine Médigue, Philippe Lehours, Jean-Charles Delchier, Laurence Ma, Jean-Michel Thiberge, Jean-Yves Coppée, Hilde De Reuse, Anne Courillon-Mallet, Aurélie Lajus, Christophe Burucoa, Josette Raymond, Agnès Labigne, Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Institut Pasteur [Paris], Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Infection à helicobacter, inflammation et cancer, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Puces à ADN (Plate-Forme 2) (PF2), Génomique (Plate-Forme) - Genomics Platform, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Inflammation, Tissus épithéliaux et Cytokines (LITEC), Université de Poitiers, CIC Saint-Antoine, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Hôpital Villeneuve Saint Georges, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Pathogenèse de Helicobacter, The Role of Peptidoglycan in Bacterial Cell Physiology: Morphology, Resistance to B-Lactams and Host-microbe Interactions, Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie et Génétique de la Paroi bactérienne - Biology and Genetics of Bacterial Cell Wall (BGPB), Hôpital Hôtel Dieu, Hôpital Henri Mondor, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Hôpital Cochin [AP-HP], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris] (IP), BMC, Ed., Intégration et Analyse Génomique (Plate-Forme), Université Bordeaux Segalen - Bordeaux 2 - Institut National de la Santé et de la Recherche Médicale (INSERM), Puces à ADN (Plate-Forme), Génomique (Plate-Forme), Commissariat à l'énergie atomique et aux énergies alternatives (CEA) - Université d'Evry-Val d'Essonne - Centre National de la Recherche Scientifique (CNRS), Bactériologie (LITEC), CHU de Poitiers, Assistance publique - Hôpitaux de Paris (AP-HP) - Institut National de la Santé et de la Recherche Médicale (INSERM) - CHU Saint-Antoine [APHP], Assistance publique - Hôpitaux de Paris (AP-HP), Biologie et Génétique de la Paroi bactérienne, Assistance publique - Hôpitaux de Paris (AP-HP) - Hôpital Henri Mondor - Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and CHU Cochin [APHP]

Subjects
MESH: Intestinal Diseases, MESH: Genome, Bacterial, Genome, MESH: Nucleic Acid Hybridization, Cluster Analysis, MESH: Genomic Islands, MESH: Lymphoma, B-Cell, Marginal Zone, MESH: Phylogeny, MESH: Bacterial Proteins, Phylogeny, MESH: Evolution, Molecular, Oligonucleotide Array Sequence Analysis, Genetics, 0303 health sciences, biology, DNA–DNA hybridization, Nucleic Acid Hybridization, MALT lymphoma, Gastritis, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Gastritis, Research Article, Biotechnology, Genomic Islands, lcsh:QH426-470, lcsh:Biotechnology, Evolution, Molecular, 03 medical and health sciences, MESH: Gene Expression Profiling, Bacterial Proteins, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], lcsh:TP248.13-248.65, medicine, Humans, MESH: Species Specificity, 030304 developmental biology, Synteny, Comparative genomics, MESH: Humans, Helicobacter pylori, 030306 microbiology, Gene Expression Profiling, Lymphoma, B-Cell, Marginal Zone, biology.organism_classification, medicine.disease, MESH: Cluster Analysis, Intestinal Diseases, lcsh:Genetics, Genetic marker, Duodenal Ulcer, MESH: Duodenal Ulcer, MESH: Oligonucleotide Array Sequence Analysis, MESH: Helicobacter pylori, Genome, Bacterial, Comparative genomic hybridization
Abstract

Background elicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach. Results A set of 254 H. pylori genes was used to perform array-based comparative genomic hybridization among 120 French H. pylori strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with cag PAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released H. pylori genomes (i.e. J99, 26695, HPAG1, P12, G27 and Shi470). B38 has the smallest H. pylori genome described thus far (1,576,758 base pairs containing 1,528 CDSs); it contains the vacA s2m2 allele and lacks the genes encoding the major virulence factors (absence of cag PAI, bab B, bab C, sab B, and hom B). Comparative genomics led to the identification of very few sequences that are unique to the B38 strain (9 intact CDSs and 7 pseudogenes). Pair-wise genomic synteny comparisons between B38 and the 6 H. pylori sequenced genomes revealed an almost complete co-linearity, never seen before between the genomes of strain Shi470 (a Peruvian isolate) and B38. Conclusion These isolates are deprived of the main H. pylori virulence factors characterized previously, but are nonetheless associated with gastric neoplasia.

Published
2010

32. Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence

Author

Eric Pelletier, Nuria Fonknechten, Jean Weissenbach, Marcel Salanoubat, Nadia Perchat, Sébastien Chaussonnerie, Sabine Tricot, Jan R. Andreesen, Denis Le Paslier, Michel Gouyvenoux, Aurélie Lajus, Georges N. Cohen, Valérie Barbe, Annett Kreimeyer, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute of Biology/Microbiology, Martin-Luther-Universität Halle Wittenberg (MLU), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]

Subjects
Clostridium sticklandii, MESH: Amino Acids, MESH: Clostridium sticklandii, MESH: Amino Acid Sequence, MESH: Base Sequence, MESH: Multienzyme Complexes, MESH: Genome, Bacterial, 7. Clean energy, Genome, Mass Spectrometry, Amino Acids, Peptide sequence, MESH: Bacterial Proteins, Conserved Sequence, chemistry.chemical_classification, Genetics, 0303 health sciences, MESH: Oxidative Stress, MESH: Conserved Sequence, biology, Stickland reaction, MESH: Energy Metabolism, MESH: Synteny, Amino acid, Biochemistry, Multigene Family, Amino Acid Oxidoreductases, Energy source, Metabolic Networks and Pathways, comic_books.character, Research Article, Biotechnology, MESH: Selenocysteine, lcsh:QH426-470, lcsh:Biotechnology, Molecular Sequence Data, MESH: Amino Acid Oxidoreductases, MESH: Sequence Alignment, Synteny, Clostridia, 03 medical and health sciences, Bacterial Proteins, Multienzyme Complexes, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Amino Acid Sequence, 030304 developmental biology, MESH: Mass Spectrometry, MESH: Molecular Sequence Data, Base Sequence, 030306 microbiology, Metabolism, biology.organism_classification, Selenocysteine, Oxidative Stress, lcsh:Genetics, chemistry, MESH: Metabolic Networks and Pathways, comic_books, MESH: Multigene Family, Energy Metabolism, Sequence Alignment, MESH: Chromatography, Liquid, Genome, Bacterial, Chromatography, Liquid
Abstract

Background Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabolic aspects such as the Stickland reaction, coenzyme-B12- and selenium-dependent reactions of amino acids. With the goal of revisiting its carbon, nitrogen, and energy metabolism, and comparing studies with other clostridia, its genome has been sequenced and analyzed. Results C. sticklandii is one of the best biochemically studied proteolytic clostridial species. Useful additional information has been obtained from the sequencing and annotation of its genome, which is presented in this paper. Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. The organism prefers threonine, arginine, serine, cysteine, proline, and glycine, whereas glutamate, aspartate and alanine are excreted. Energy conservation is primarily obtained by substrate-level phosphorylation in fermentative pathways. The reactions catalyzed by different ferredoxin oxidoreductases and the exergonic NADH-dependent reduction of crotonyl-CoA point to a possible chemiosmotic energy conservation via the Rnf complex. C. sticklandii possesses both the F-type and V-type ATPases. The discovery of an as yet unrecognized selenoprotein in the D-proline reductase operon suggests a more detailed mechanism for NADH-dependent D-proline reduction. A rather unusual metabolic feature is the presence of genes for all the enzymes involved in two different CO2-fixation pathways: C. sticklandii harbours both the glycine synthase/glycine reductase and the Wood-Ljungdahl pathways. This unusual pathway combination has retrospectively been observed in only four other sequenced microorganisms. Conclusions Analysis of the C. sticklandii genome and additional experimental procedures have improved our understanding of anaerobic amino acid degradation. Several specific metabolic features have been detected, some of which are very unusual for anaerobic fermenting bacteria. Comparative genomics has provided the opportunity to study the lifestyle of pathogenic and non-pathogenic clostridial species as well as to elucidate the difference in metabolic features between clostridia and other anaerobes.

Published
2010

33. Genome sequence of the obligate methanotroph methylosinus trichosporium strain ob3b

Author

Lisa Y. Stein, Miriam Land, Mike S. M. Jetten, Susan Lucas, Ahmet Zeytun, Lynne Goodwin, Jeremy D. Semrau, Marina G. Kalyuzhnaya, Martin G. Klotz, Claudine Médigue, Françoise Bringel, Huub J. M. Op den Camp, Tanja Woyke, Alex Copeland, J. Colin Murrell, Sukhwan Yoon, Samuel Pitluck, Shunsheng Han, Andrew T. Crombie, Alan A. DiSpirito, Aurélie Lajus, Alla Lapidus, David Bruce, Jan Fang Cheng, Loren Hauser, Stéphane Vuilleumier, University of Alberta, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
Methanotroph, Methane monooxygenase, Molecular Sequence Data, Context (language use), Microbiology, 03 medical and health sciences, Bacterial Proteins, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, Obligate, 030306 microbiology, Methanobactin, Gene Expression Regulation, Bacterial, biology.organism_classification, Methylosinus trichosporium, 3. Good health, Genome Announcements, Biochemistry, Ecological Microbiology, Anaerobic oxidation of methane, Methylocystaceae, biology.protein, Bacteria, Genome, Bacterial
Abstract

Methylosinus trichosporium OB3b (for “oddball” strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This strain has since been used extensively to elucidate the structure and function of several key enzymes of methane oxidation, including both particulate and soluble methane monooxygenase (sMMO) and the extracellular copper chelator methanobactin. In particular, the catalytic properties of soluble methane monooxygenase from M. trichosporium OB3b have been well characterized in context with biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of the M. trichosporium OB3b genome is the first reported from a member of the Methylocystaceae family in the order Rhizobiales .

Published
2010

34. Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity

Author

Christophe Rusniok, Martin F. Polz, Frédérique Le Roux, Nesrine Chakroun, Denis Saulnier, Mohamed Zouine, Didier Mazel, Laurence Ma, Nora Zidane, Christiane Bouchier, Carmen Buchrieser, Claudine Médigue, Johan Binesse, and Aurélie Lajus

Subjects
Molecular Sequence Data, Integron, Microbiology, Genome, Integrons, 03 medical and health sciences, Phylogenetics, Genetic variation, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Vibrio, Whole genome sequencing, Genetics, 0303 health sciences, Genetic diversity, biology, Base Sequence, 030306 microbiology, Trimethoprim Resistance, Chromosome, Genetic Variation, Biodiversity, biology.organism_classification, DNA Fingerprinting, biology.protein, Genome, Bacterial
Abstract

P>Vibrio splendidus is a dominant Vibrio species in seawater presenting a remarkable genetic diversity; several strains have been linked to invertebrate's mortality. We report the complete genome sequence of V. splendidus LGP32, an oyster pathogen, and its comparison with partial genome sequences from related strains. As is typical for the genus, V. splendidus LGP32 contains two chromosomes (3.29 and 1.67 Mb) and most essential cellular processes are encoded by chromosome 1. Comparison with two other V. splendidus partial genome sequences (strains 12B01 and Med222) confirms the previously suggested high genotypic diversity within this species and led to the identification of numerous strain-specific regions that could frequently not be assigned to a specific mechanisms of recombination. Surprisingly, the chromosomal integron, the most variable genetic element in all other Vibrio species analysed to date, is absent from 12B01 and inactivated by a mobile element in Med222, while in LGP32 it only contains a limited number of cassettes. Finally, we found that the LGP32 integron contains a new dfrA cassette, related to those found in resistance integrons of Gram-negative clinical isolates. Those results suggest that marine Vibrio can be a source of antibiotic resistance genes.

Published
2009

35. NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis

Author

Coralie Mouzé-Soulama, Stéphanie Floquet, Daniel R. Brown, Vladimir Pelicic, Helen A. Ewles, David Vallenet, Aurélie Lajus, Philippe Glaser, Christophe Rusniok, Carmen Buchrieser, Claudine Médigue, Génomique des Microorganismes Pathogènes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Imperial College London, INSERM, Institut Pasteur/CHU Necker-Enfants Malades, MRT and ANR, BMC, Ed., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Department of Microbiology, CMMI, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Pathogénie des infections systémiques ( UMR_S 570 ), and Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
MESH: Sequence Analysis, DNA, Colony Count, Microbial, Fluorescent Antibody Technique, Human pathogen, [SDV.GEN] Life Sciences [q-bio]/Genetics, Neisseria meningitidis, MESH: Base Sequence, MESH: Virulence, medicine.disease_cause, Genome, Nasopharynx, MESH : Bacterial Proteins, MESH: Bacterial Proteins, MESH: Fluorescent Antibody Technique, MESH: Microbial Viability, Genetics, 0303 health sciences, Virulence, MESH : Genes, Bacterial, MESH: Genomics, MESH : Virulence, Genomics, 3. Good health, MESH: DNA Transposable Elements, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Multigene Family, MESH : DNA Transposable Elements, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH : Software, MESH : Mutation, MESH: Genes, Bacterial, MESH: Mutation, Sequence analysis, MESH : Colony Count, Microbial, MESH : Multigene Family, Biology, MESH: Sequence Homology, Nucleic Acid, MESH: Neisseria meningitidis, Bacterial genetics, 03 medical and health sciences, MESH: Software, Bacterial Proteins, Sequence Homology, Nucleic Acid, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Humans, MESH : Sequence Homology, Nucleic Acid, Gene, MESH: Colony Count, Microbial, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Microbial Viability, MESH: Humans, Base Sequence, 030306 microbiology, MESH : Neisseria meningitidis, Research, MESH : Genomics, MESH : Humans, MESH : Microbial Viability, Sequence Analysis, DNA, Human genetics, MESH: Nasopharynx, MESH : Fluorescent Antibody Technique, Genes, Bacterial, Mutation, DNA Transposable Elements, MESH : Nasopharynx, MESH: Multigene Family, MESH : Base Sequence, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, Software, MESH : Sequence Analysis, DNA
Abstract

The genome of a clinical isolate of Neisseria meningitidis is described. This and other reannotated Neisseria genomes are compiled in a database., Background Genome sequences, now available for most pathogens, hold promise for the rational design of new therapies. However, biological resources for genome-scale identification of gene function (notably genes involved in pathogenesis) and/or genes essential for cell viability, which are necessary to achieve this goal, are often sorely lacking. This holds true for Neisseria meningitidis, one of the most feared human bacterial pathogens that causes meningitis and septicemia. Results By determining and manually annotating the complete genome sequence of a serogroup C clinical isolate of N. meningitidis (strain 8013) and assembling a library of defined mutants in up to 60% of its non-essential genes, we have created NeMeSys, a biological resource for Neisseria meningitidis systematic functional analysis. To further enhance the versatility of this toolbox, we have manually (re)annotated eight publicly available Neisseria genome sequences and stored all these data in a publicly accessible online database. The potential of NeMeSys for narrowing the gap between sequence and function is illustrated in several ways, notably by performing a functional genomics analysis of the biogenesis of type IV pili, one of the most widespread virulence factors in bacteria, and by identifying through comparative genomics a complete biochemical pathway (for sulfur metabolism) that may potentially be important for nasopharyngeal colonization. Conclusions By improving our capacity to understand gene function in an important human pathogen, NeMeSys is expected to contribute to the ongoing efforts aimed at understanding a prokaryotic cell comprehensively and eventually to the design of new therapies.

Published
2009

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

Author

Claudine Médigue, Delphine Capela, Chantal Schenowitz, Catherine Masson-Boivin, Sébastien Carrère, Valérie Barbe, Marta Marchetti, Zoé Rouy, Claire Amadou, Bertrand Servin, Aurélie Lajus, Jacques Batut, Carole Dossat, Maged M. Saad, Géraldine Pascal, Sophie Mangenot, Véréna Poinsot, Stéphane Cruveiller, Michelle D. Glew, Cyril Bontemps, Departement /u563 : Immunologie et Maladies infectieuses, Centre de Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Département d'Astrophysique, de physique des Particules, de physique Nucléaire et de l'Instrumentation Associée (DAPNIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre d'études techniques de l'équipement Est (CETE Est), Avant création Cerema, Interactions moléculaires et réactivité chimique et photochimique (IMRCP), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre de Physiopathologie Toulouse Purpan ex IFR 30 et IFR 150 (CPTP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

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

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

Published
2008

37. Legumes Symbioses: Absence of Nod Genes in Photosynthetic Bradyrhizobia

Author

Béatrice Segurens, Paul G. Richardson, Jean-Christophe Avarre, Bernard Dreyfus, Eddie Cytryn, Joël Fardoux, William L. Franck, Woo Suk Chang, Lionel Moulin, Zoé Rouy, Yves Prin, Philippe Normand, David Vallenet, Fabienne Cartieaux, Carole Dossat, Gilles Béna, Elizabeth Saunders, Claudine Médigue, Eric Giraud, Damien Simon, Marianne Jaubert, Michael J. Sadowsky, Aurélie Lajus, David Bruce, Laura Hannibal, André Verméglio, Laurie Vuillet, Mila Kojadinovic, Stéphane Cruveiller, Sophie Mangenot, David W. Emerich, David Pignol, Gary Stacey, Valérie Barbe, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de Séquençage, Université d'Évry-Val-d'Essonne (UEVE), department of soil, Biotechnology institute-Saint Mary's University of Minnesota, Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), National Center of Soybean Biotechnology, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Commisariat à lEnergie Atomique ((CEA)), Université de la Méditerranée - Aix-Marseille 2, Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Missouri [Columbia], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire des symbioses tropicales et méditerranéennes ( LSTM ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université Montpellier 1 ( UM1 ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Université d'Évry-Val-d'Essonne ( UEVE ), Laboratoire d'Intégration des Systèmes et des Technologies ( LIST ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Structure et évolution des génomes ( SEG ), CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), University of Missouri-Columbia, Department of Energy / Joint Genome Institute ( DOE ), Los Alamos National Laboratory ( LANL ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Commisariat à lEnergie Atomique ( (CEA) ), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Lipopolysaccharides, Root nodule, Cytokinins, Bradyrhizobium japonicum, nodosité racinaire, [SDE.BE.ECO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.eco, Plant Roots, F30 - Génétique et amélioration des plantes, Nod factor, Bradyrhizobium, Photosynthesis, Genetics, 0303 health sciences, Multidisciplinary, biology, Plant Stems, Formation de nodosités, food and beverages, Fabaceae, Genomics, [ SDE.BE.ECO ] Environmental Sciences/Biodiversity and Ecology/domain_sde.be.eco, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Root Nodules, Plant, Signal Transduction, Séquence nucléotidique, Rhizobiaceae, Molecular Sequence Data, Symbiose, N-Acetylglucosaminyltransferases, Rhizobia, Amidohydrolases, 03 medical and health sciences, Symbiosis, Bacterial Proteins, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Rhizobactérie, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Génome, 030306 microbiology, Mutant, P34 - Biologie du sol, Biologie moléculaire, biology.organism_classification, Genes, Bacterial, Purines, Mutation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Acyltransferases, Genome, Bacterial
Abstract

Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.

Published
2007

38. A Genomic Island of the Pathogen Leptospira interrogans Serovar Lai Can Excise from Its Chromosome▿ †

Author

Claudine Médigue, Pascale Bourhy, Caroline Boursaux-Eude, Laurence Salaün, Aurélie Lajus, and Mathieu Picardeau

Subjects
DNA Replication, DNA, Bacterial, Genomic Islands, Immunology, Genetic Vectors, Molecular Sequence Data, Sequence Homology, Locus (genetics), Genomics, Molecular Genomics, Biology, Microbiology, Genome, Open Reading Frames, Plasmid, Shuttle vector, Genomic island, Cloning, Molecular, Gene, Genetics, Recombination, Genetic, Computational Biology, Sequence Analysis, DNA, Chromosomes, Bacterial, biology.organism_classification, Molecular biology, Electrophoresis, Gel, Pulsed-Field, Infectious Diseases, Genes, Bacterial, Parasitology, Leptospira interrogans, Plasmids
Abstract

An examination of the two Leptospira interrogans genomes sequenced so far reveals few genetic differences, including an extra DNA region, 54 kb in length, in L. interrogans serovar Lai. This locus contains 103 predicted coding sequences that are absent from the genome of L. interrogans serovar Copenhageni, of which only 20% had significant BLASTP hits in GenBank. By analyzing the L. interrogans serovar Lai genome by pulsed-field gel electrophoresis, we also found that this 54-kb DNA fragment exists as a circular plasmid. This was confirmed by amplification of a DNA fragment corresponding to that of the predicted fragment if this region excised from the chromosome and its left and right ends joined together. In addition, cloning of the putative rep gene of this DNA region was responsible for autonomous replication in Leptospira spp., therefore generating a new Escherichia coli-Leptospira sp. shuttle vector. Taken together, our results show that this genomic island can excise from the chromosome and form a replicative plasmid. Analysis of the distribution of this genomic island revealed that highly related sequences exist in other L. interrogans virulent strains. This genomic island, containing a high proportion of novel genes, may have an important role in spreading genes, including virulence factors, among bacterial populations.

Published
2006

39. Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila

Author

David Vallenet, Bruno Lemaitre, Claire Jubin, Claudine Médigue, Zoé Rouy, Nicolas Vodovar, Patrick Wincker, Aurélie Lajus, Béatrice Ségurens, Benoit Vacherie, Stéphane Cruveiller, Valérie Barbe, Laurence Cattolico, Jean Weissenbach, Frédéric Boccard, Carlos Acosta, Centre de génétique moléculaire (CGM), Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and CNRS (Programme Séquençage à grande échelle), IFR115, MRT/ACI IMPBio 2004 ‘MicroScope', N.V. was supported by a doctoral fellowship from the Association Vaincre la Mucoviscidose and the Association pour la Recherche sur le Cancer (ARC)

Subjects
Insecticides, Insecta, Molecular Sequence Data, Biomedical Engineering, Virulence, Bioengineering, MESH: Base Sequence, MESH: Genome, Bacterial, Applied Microbiology and Biotechnology, Genome, Microbiology, 03 medical and health sciences, Complete sequence, MESH: Insects, Bacterial Proteins, Pseudomonas, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, MESH: Pest Control, Biological, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Pest Control, Biological, Pathogen, MESH: Bacterial Proteins, Soil Microbiology, 030304 developmental biology, 0303 health sciences, MESH: Molecular Sequence Data, Base Sequence, biology, 030306 microbiology, Chromosome Mapping, MESH: Pseudomonas, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Insecticides, MESH: Soil Microbiology, Pseudomonadales, Molecular Medicine, MESH: Chromosome Mapping, Pseudomonas entomophila, Genome, Bacterial, Biotechnology, Pseudomonadaceae
Abstract

Pseudomonas entomophila is an entomopathogenic bacterium that, upon ingestion, kills Drosophila melanogaster as well as insects from different orders. The complete sequence of the 5.9-Mb genome was determined and compared to the sequenced genomes of four Pseudomonas species. P. entomophila possesses most of the catabolic genes of the closely related strain P. putida KT2440, revealing its metabolically versatile properties and its soil lifestyle. Several features that probably contribute to its entomopathogenic properties were disclosed. Unexpectedly for an animal pathogen, P. entomophila is devoid of a type III secretion system and associated toxins but rather relies on a number of potential virulence factors such as insecticidal toxins, proteases, putative hemolysins, hydrogen cyanide and novel secondary metabolites to infect and kill insects. Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified.

Published
2006

40. Sequencing of K60, Type Strain of the Major Plant Pathogen Ralstonia solanacearum

Author

Philippe Prior, Aurélie Lajus, Lavanya Babujee, Benoît Remenant, Claudine Médigue, Caitilyn Allen, University of Wisconsin-Madison, Centre National de la Recherche Scientifique (CNRS), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Molecular Sequence Data, 01 natural sciences, Microbiology, Genome, 03 medical and health sciences, Solanum lycopersicum, Molecular Biology, Pathogen, Gene, ComputingMilieux_MISCELLANEOUS, Plant Diseases, 030304 developmental biology, Phylotype, 0303 health sciences, Ralstonia solanacearum, biology, Bacterial wilt, Strain (biology), fungi, food and beverages, Outbreak, Gene Expression Regulation, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, United States, Genome Announcements, Caribbean Region, [SDE]Environmental Sciences, Genome, Bacterial, 010606 plant biology & botany
Abstract

Ralstonia solanacearum is a widespread and destructive plant pathogen. We present the genome of the type strain, K60 (phylotype IIA, sequevar 7). Sequevar 7 strains cause ongoing tomato bacterial wilt outbreaks in the southeastern United States. K60 generally resembles R. solanacearum CFBP2957, a Caribbean tomato isolate, but has almost 360 unique genes.

Published
2012

41. Draft genome sequence of the volcano-inhabiting thermoacidophilic methanotroph methylacidiphilum fumariolicum strain solv

Author

Lisa Y. Stein, Martin G. Klotz, J. Colin Murrell, Alan A. DiSpirito, Stéphane Vuilleumier, Aurélie Lajus, Henk Stunnenberg, Arjan Pol, Harry R. Harhangi, Jeremy D. Semrau, Adam S. Wieczorek, Ahmad F. Khadem, Marina G. Kalyuzhnaya, Mike S. M. Jetten, Kees Jan Francoijs, Claudine Médigue, Huub J. M. Op den Camp, and Peter F. Dunfield

Subjects
Whole genome sequencing, Genetics, Geological Phenomena, Methanotroph, Strain (biology), Molecular Sequence Data, Verrucomicrobia, Biology, biology.organism_classification, Microbiology, Phylum Verrucomicrobia, Genome, Genome Announcements, Metabolic pathway, Ecological Microbiology, Methylacidiphilum fumariolicum, Molecular Biology, Genome, Bacterial
Abstract

The draft genome of Methylacidiphilum fumariolicum SolV, a thermoacidophilic methanotroph of the phylum Verrucomicrobia , is presented. Annotation revealed pathways for one-carbon, nitrogen, and hydrogen catabolism and respiration together with central metabolic pathways. The genome encodes three orthologues of particulate methane monooxygenases. Sequencing of this genome will help in the understanding of methane cycling in volcanic environments.

Published
2012

42. Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis

Author

Christiane Bouchier, Ben Adler, Zoé Rouy, Elizabeth Kuczek, John Davis, Matthew Johnson, Caroline Boursaux-Eude, Dieter M. Bulach, Claudine Médigue, John K. Davies, Peter Wilson, Nora Zidane, Richard L. Zuerner, Torsten Seemann, Ross L. Coppel, Sophie Creno, Mathieu Picardeau, Aurélie Lajus, Annette McGrath, Simona Bommezzadri, Julian I. Rood, Biologie des Spirochètes / Biology of Spirochetes, Institut Pasteur [Paris], Monash University [Clayton], Génomique (Plate-Forme) - Genomics Platform, USDA-ARS : Agricultural Research Service, Bioanalyse génomique (Plate-Forme), University of Queensland [Brisbane], Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), This work was supported by the following: National Health and Medical Research Council, Australia, Australian Research Council, U.S. Department of Agriculture, Institut Pasteur, Paris, France, French Ministry of Research ANR Jeunes Chercheurs (no. 05-JCJC-0105-01), Consortium National de Recherche en Génomique (no. RNG-20040057), ACI IMPBio 2004 (MicroScope project)., We thank David Alt, Richard Hornsby, A. Magnier and A. Blanchard for technical support., ANR-05-JCJC-0105,leptospirose,Identification des facteurs de virulence des leptospires, bactéries pathogènes(2005), Institut Pasteur [Paris] (IP), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Genome evolution, Science, Genome, Insect, Genes, Insect, Biology, Genome, 03 medical and health sciences, Leptospira, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene density, Leptospirosis, Gene, 030304 developmental biology, Gene Rearrangement, Genetics, Comparative genomics, 0303 health sciences, Microbiology/Microbial Evolution and Genomics, Multidisciplinary, Base Sequence, 030306 microbiology, Microbiology/Medical Microbiology, Gene rearrangement, biology.organism_classification, Biological Evolution, Medicine, Microbiology/Cellular Microbiology and Pathogenesis, Leptospira interrogans, Research Article, Signal Transduction
Abstract

International audience; Leptospira biflexa is a free-living saprophytic spirochete present in aquatic environments. We determined the genome sequence of L. biflexa, making it the first saprophytic Leptospira to be sequenced. The L. biflexa genome has 3,590 protein-coding genes distributed across three circular replicons: the major 3,604 chromosome, a smaller 278-kb replicon that also carries essential genes, and a third 74-kb replicon. Comparative sequence analysis provides evidence that L. biflexa is an excellent model for the study of Leptospira evolution; we conclude that 2052 genes (61%) represent a progenitor genome that existed before divergence of pathogenic and saprophytic Leptospira species. Comparisons of the L. biflexa genome with two pathogenic Leptospira species reveal several major findings. Nearly one-third of the L. biflexa genes are absent in pathogenic Leptospira. We suggest that once incorporated into the L. biflexa genome, laterally transferred DNA undergoes minimal rearrangement due to physical restrictions imposed by high gene density and limited presence of transposable elements. In contrast, the genomes of pathogenic Leptospira species undergo frequent rearrangements, often involving recombination between insertion sequences. Identification of genes common to the two pathogenic species, L. borgpetersenii and L. interrogans, but absent in L. biflexa, is consistent with a role for these genes in pathogenesis. Differences in environmental sensing capacities of L. biflexa, L. borgpetersenii, and L. interrogans suggest a model which postulates that loss of signal transduction functions in L. borgpetersenii has impaired its survival outside a mammalian host, whereas L. interrogans has retained environmental sensory functions that facilitate disease transmission through water.

Published
2008

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